Starting phenix.real_space_refine on Sun Jun 7 03:00:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p9l_71417/06_2026/9p9l_71417.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p9l_71417/06_2026/9p9l_71417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p9l_71417/06_2026/9p9l_71417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p9l_71417/06_2026/9p9l_71417.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p9l_71417/06_2026/9p9l_71417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p9l_71417/06_2026/9p9l_71417.map" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 S 270 5.16 5 Cl 18 4.86 5 C 20796 2.51 5 N 5742 2.21 5 O 6180 1.98 5 F 180 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33192 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "B" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "C" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "D" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "E" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "F" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "G" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "H" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "I" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "J" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "K" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "L" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "M" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "N" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "O" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "P" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "Q" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "R" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 211} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 100 Unusual residues: {'IHP': 1, 'QNG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'QNG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "L" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "O" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 8.26, per 1000 atoms: 0.25 Number of scatterers: 33192 At special positions: 0 Unit cell: (172.581, 167.215, 115.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 18 17.00 S 270 16.00 P 6 15.00 F 180 9.00 O 6180 8.00 N 5742 7.00 C 20796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.4 seconds 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7632 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 0 sheets defined 74.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.650A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.619A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 223 through 238 Processing helix chain 'B' and resid 16 through 31 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 193 removed outlier: 3.649A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.619A pdb=" N GLY B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 223 through 238 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 175 Processing helix chain 'C' and resid 178 through 193 removed outlier: 3.649A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.619A pdb=" N GLY C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'C' and resid 223 through 238 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 119 Processing helix chain 'D' and resid 125 through 145 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 175 Processing helix chain 'D' and resid 178 through 193 removed outlier: 3.649A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.618A pdb=" N GLY D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'D' and resid 223 through 238 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 125 through 145 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 178 through 193 removed outlier: 3.650A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.619A pdb=" N GLY E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'E' and resid 223 through 238 Processing helix chain 'F' and resid 16 through 31 Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 119 Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 175 Processing helix chain 'F' and resid 178 through 193 removed outlier: 3.649A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.619A pdb=" N GLY F 206 " --> pdb=" O LEU F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 218 Processing helix chain 'F' and resid 223 through 238 Processing helix chain 'G' and resid 16 through 31 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 119 Processing helix chain 'G' and resid 125 through 145 Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 175 Processing helix chain 'G' and resid 178 through 193 removed outlier: 3.649A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.618A pdb=" N GLY G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 218 Processing helix chain 'G' and resid 223 through 238 Processing helix chain 'H' and resid 16 through 31 Processing helix chain 'H' and resid 35 through 44 Processing helix chain 'H' and resid 48 through 58 Processing helix chain 'H' and resid 62 through 84 Processing helix chain 'H' and resid 100 through 105 Processing helix chain 'H' and resid 110 through 119 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'H' and resid 149 through 153 Processing helix chain 'H' and resid 160 through 175 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.648A pdb=" N LEU H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 206 removed outlier: 3.619A pdb=" N GLY H 206 " --> pdb=" O LEU H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'H' and resid 223 through 238 Processing helix chain 'I' and resid 16 through 31 Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 48 through 58 Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 110 through 119 Processing helix chain 'I' and resid 125 through 145 Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 175 Processing helix chain 'I' and resid 178 through 193 removed outlier: 3.648A pdb=" N LEU I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 206 removed outlier: 3.618A pdb=" N GLY I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 218 Processing helix chain 'I' and resid 223 through 238 Processing helix chain 'J' and resid 16 through 31 Processing helix chain 'J' and resid 35 through 44 Processing helix chain 'J' and resid 48 through 58 Processing helix chain 'J' and resid 62 through 84 Processing helix chain 'J' and resid 100 through 105 Processing helix chain 'J' and resid 110 through 119 Processing helix chain 'J' and resid 125 through 145 Processing helix chain 'J' and resid 149 through 153 Processing helix chain 'J' and resid 160 through 175 Processing helix chain 'J' and resid 178 through 193 removed outlier: 3.649A pdb=" N LEU J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL J 191 " --> pdb=" O GLU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 206 removed outlier: 3.618A pdb=" N GLY J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 218 Processing helix chain 'J' and resid 223 through 238 Processing helix chain 'K' and resid 16 through 31 Processing helix chain 'K' and resid 35 through 44 Processing helix chain 'K' and resid 48 through 58 Processing helix chain 'K' and resid 62 through 84 Processing helix chain 'K' and resid 100 through 105 Processing helix chain 'K' and resid 110 through 119 Processing helix chain 'K' and resid 125 through 145 Processing helix chain 'K' and resid 149 through 153 Processing helix chain 'K' and resid 160 through 175 Processing helix chain 'K' and resid 178 through 193 removed outlier: 3.648A pdb=" N LEU K 190 " --> pdb=" O THR K 186 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 206 removed outlier: 3.619A pdb=" N GLY K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 218 Processing helix chain 'K' and resid 223 through 238 Processing helix chain 'L' and resid 16 through 31 Processing helix chain 'L' and resid 35 through 44 Processing helix chain 'L' and resid 48 through 58 Processing helix chain 'L' and resid 62 through 84 Processing helix chain 'L' and resid 100 through 105 Processing helix chain 'L' and resid 110 through 119 Processing helix chain 'L' and resid 125 through 145 Processing helix chain 'L' and resid 149 through 153 Processing helix chain 'L' and resid 160 through 175 Processing helix chain 'L' and resid 178 through 193 removed outlier: 3.649A pdb=" N LEU L 190 " --> pdb=" O THR L 186 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 206 removed outlier: 3.618A pdb=" N GLY L 206 " --> pdb=" O LEU L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 218 Processing helix chain 'L' and resid 223 through 238 Processing helix chain 'M' and resid 16 through 31 Processing helix chain 'M' and resid 35 through 44 Processing helix chain 'M' and resid 48 through 58 Processing helix chain 'M' and resid 62 through 84 Processing helix chain 'M' and resid 100 through 105 Processing helix chain 'M' and resid 110 through 119 Processing helix chain 'M' and resid 125 through 145 Processing helix chain 'M' and resid 149 through 153 Processing helix chain 'M' and resid 160 through 175 Processing helix chain 'M' and resid 178 through 193 removed outlier: 3.648A pdb=" N LEU M 190 " --> pdb=" O THR M 186 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL M 191 " --> pdb=" O GLU M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 206 removed outlier: 3.619A pdb=" N GLY M 206 " --> pdb=" O LEU M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 218 Processing helix chain 'M' and resid 223 through 238 Processing helix chain 'N' and resid 16 through 31 Processing helix chain 'N' and resid 35 through 44 Processing helix chain 'N' and resid 48 through 58 Processing helix chain 'N' and resid 62 through 84 Processing helix chain 'N' and resid 100 through 105 Processing helix chain 'N' and resid 110 through 119 Processing helix chain 'N' and resid 125 through 145 Processing helix chain 'N' and resid 149 through 153 Processing helix chain 'N' and resid 160 through 175 Processing helix chain 'N' and resid 178 through 193 removed outlier: 3.648A pdb=" N LEU N 190 " --> pdb=" O THR N 186 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL N 191 " --> pdb=" O GLU N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 206 removed outlier: 3.619A pdb=" N GLY N 206 " --> pdb=" O LEU N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 218 Processing helix chain 'N' and resid 223 through 238 Processing helix chain 'O' and resid 16 through 31 Processing helix chain 'O' and resid 35 through 44 Processing helix chain 'O' and resid 48 through 58 Processing helix chain 'O' and resid 62 through 84 Processing helix chain 'O' and resid 100 through 105 Processing helix chain 'O' and resid 110 through 119 Processing helix chain 'O' and resid 125 through 145 Processing helix chain 'O' and resid 149 through 153 Processing helix chain 'O' and resid 160 through 175 Processing helix chain 'O' and resid 178 through 193 removed outlier: 3.648A pdb=" N LEU O 190 " --> pdb=" O THR O 186 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL O 191 " --> pdb=" O GLU O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 206 removed outlier: 3.619A pdb=" N GLY O 206 " --> pdb=" O LEU O 202 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 218 Processing helix chain 'O' and resid 223 through 238 Processing helix chain 'P' and resid 16 through 31 Processing helix chain 'P' and resid 35 through 44 Processing helix chain 'P' and resid 48 through 58 Processing helix chain 'P' and resid 62 through 84 Processing helix chain 'P' and resid 100 through 105 Processing helix chain 'P' and resid 110 through 119 Processing helix chain 'P' and resid 125 through 145 Processing helix chain 'P' and resid 149 through 153 Processing helix chain 'P' and resid 160 through 175 Processing helix chain 'P' and resid 178 through 193 removed outlier: 3.650A pdb=" N LEU P 190 " --> pdb=" O THR P 186 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL P 191 " --> pdb=" O GLU P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 206 removed outlier: 3.619A pdb=" N GLY P 206 " --> pdb=" O LEU P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 218 Processing helix chain 'P' and resid 223 through 238 Processing helix chain 'Q' and resid 16 through 31 Processing helix chain 'Q' and resid 35 through 44 Processing helix chain 'Q' and resid 48 through 58 Processing helix chain 'Q' and resid 62 through 84 Processing helix chain 'Q' and resid 100 through 105 Processing helix chain 'Q' and resid 110 through 119 Processing helix chain 'Q' and resid 125 through 145 Processing helix chain 'Q' and resid 149 through 153 Processing helix chain 'Q' and resid 160 through 175 Processing helix chain 'Q' and resid 178 through 193 removed outlier: 3.649A pdb=" N LEU Q 190 " --> pdb=" O THR Q 186 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL Q 191 " --> pdb=" O GLU Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 206 removed outlier: 3.619A pdb=" N GLY Q 206 " --> pdb=" O LEU Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 218 Processing helix chain 'Q' and resid 223 through 238 Processing helix chain 'R' and resid 16 through 31 Processing helix chain 'R' and resid 35 through 44 Processing helix chain 'R' and resid 48 through 58 Processing helix chain 'R' and resid 62 through 84 Processing helix chain 'R' and resid 100 through 105 Processing helix chain 'R' and resid 110 through 119 Processing helix chain 'R' and resid 125 through 145 Processing helix chain 'R' and resid 149 through 153 Processing helix chain 'R' and resid 160 through 175 Processing helix chain 'R' and resid 178 through 193 removed outlier: 3.649A pdb=" N LEU R 190 " --> pdb=" O THR R 186 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL R 191 " --> pdb=" O GLU R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 206 removed outlier: 3.619A pdb=" N GLY R 206 " --> pdb=" O LEU R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 218 Processing helix chain 'R' and resid 223 through 238 2106 hydrogen bonds defined for protein. 6210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.89 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5477 1.30 - 1.43: 8752 1.43 - 1.56: 19174 1.56 - 1.69: 23 1.69 - 1.83: 504 Bond restraints: 33930 Sorted by residual: bond pdb=" C3 IHP A 302 " pdb=" O13 IHP A 302 " ideal model delta sigma weight residual 1.393 1.203 0.190 2.00e-02 2.50e+03 9.03e+01 bond pdb=" O16 IHP A 302 " pdb=" P6 IHP A 302 " ideal model delta sigma weight residual 1.672 1.553 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C1 IHP A 302 " pdb=" O11 IHP A 302 " ideal model delta sigma weight residual 1.392 1.280 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C28 QNG K 301 " pdb=" N43 QNG K 301 " ideal model delta sigma weight residual 1.344 1.452 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C28 QNG I 301 " pdb=" N43 QNG I 301 " ideal model delta sigma weight residual 1.344 1.452 -0.108 2.00e-02 2.50e+03 2.93e+01 ... (remaining 33925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.37: 45829 5.37 - 10.73: 449 10.73 - 16.10: 120 16.10 - 21.46: 48 21.46 - 26.83: 18 Bond angle restraints: 46464 Sorted by residual: angle pdb=" C31 QNG H 301 " pdb=" C36 QNG H 301 " pdb=" C39 QNG H 301 " ideal model delta sigma weight residual 113.86 140.69 -26.83 3.00e+00 1.11e-01 8.00e+01 angle pdb=" C31 QNG R 301 " pdb=" C36 QNG R 301 " pdb=" C39 QNG R 301 " ideal model delta sigma weight residual 113.86 140.64 -26.78 3.00e+00 1.11e-01 7.97e+01 angle pdb=" C31 QNG K 301 " pdb=" C36 QNG K 301 " pdb=" C39 QNG K 301 " ideal model delta sigma weight residual 113.86 140.63 -26.77 3.00e+00 1.11e-01 7.96e+01 angle pdb=" C31 QNG I 301 " pdb=" C36 QNG I 301 " pdb=" C39 QNG I 301 " ideal model delta sigma weight residual 113.86 140.57 -26.71 3.00e+00 1.11e-01 7.93e+01 angle pdb=" C31 QNG Q 301 " pdb=" C36 QNG Q 301 " pdb=" C39 QNG Q 301 " ideal model delta sigma weight residual 113.86 140.56 -26.70 3.00e+00 1.11e-01 7.92e+01 ... (remaining 46459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.77: 19676 29.77 - 59.55: 1052 59.55 - 89.32: 388 89.32 - 119.09: 17 119.09 - 148.86: 5 Dihedral angle restraints: 21138 sinusoidal: 9330 harmonic: 11808 Sorted by residual: dihedral pdb=" C16 QNG D 301 " pdb=" N17 QNG D 301 " pdb=" S48 QNG D 301 " pdb=" O51 QNG D 301 " ideal model delta sinusoidal sigma weight residual 186.92 38.06 148.86 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" C16 QNG D 301 " pdb=" N17 QNG D 301 " pdb=" S48 QNG D 301 " pdb=" C49 QNG D 301 " ideal model delta sinusoidal sigma weight residual 302.76 160.06 142.70 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C16 QNG D 301 " pdb=" N17 QNG D 301 " pdb=" S48 QNG D 301 " pdb=" O50 QNG D 301 " ideal model delta sinusoidal sigma weight residual 59.12 -72.16 131.28 1 3.00e+01 1.11e-03 1.77e+01 ... (remaining 21135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 4939 0.164 - 0.329: 38 0.329 - 0.493: 14 0.493 - 0.657: 1 0.657 - 0.821: 18 Chirality restraints: 5010 Sorted by residual: chirality pdb=" C36 QNG H 301 " pdb=" C31 QNG H 301 " pdb=" C37 QNG H 301 " pdb=" C39 QNG H 301 " both_signs ideal model delta sigma weight residual True 2.69 1.87 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" C36 QNG Q 301 " pdb=" C31 QNG Q 301 " pdb=" C37 QNG Q 301 " pdb=" C39 QNG Q 301 " both_signs ideal model delta sigma weight residual True 2.69 1.87 0.82 2.00e-01 2.50e+01 1.67e+01 chirality pdb=" C36 QNG K 301 " pdb=" C31 QNG K 301 " pdb=" C37 QNG K 301 " pdb=" C39 QNG K 301 " both_signs ideal model delta sigma weight residual True 2.69 1.87 0.82 2.00e-01 2.50e+01 1.67e+01 ... (remaining 5007 not shown) Planarity restraints: 5886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C07 QNG D 301 " 0.044 2.00e-02 2.50e+03 1.57e-02 8.05e+00 pdb=" C08 QNG D 301 " 0.003 2.00e-02 2.50e+03 pdb=" C09 QNG D 301 " -0.002 2.00e-02 2.50e+03 pdb=" C10 QNG D 301 " -0.007 2.00e-02 2.50e+03 pdb=" C11 QNG D 301 " -0.001 2.00e-02 2.50e+03 pdb=" C12 QNG D 301 " 0.005 2.00e-02 2.50e+03 pdb=" C13 QNG D 301 " -0.032 2.00e-02 2.50e+03 pdb=" C16 QNG D 301 " 0.001 2.00e-02 2.50e+03 pdb=" C18 QNG D 301 " -0.008 2.00e-02 2.50e+03 pdb=" N14 QNG D 301 " 0.004 2.00e-02 2.50e+03 pdb=" N15 QNG D 301 " 0.002 2.00e-02 2.50e+03 pdb=" N17 QNG D 301 " -0.001 2.00e-02 2.50e+03 pdb="CL47 QNG D 301 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 QNG M 301 " 0.041 2.00e-02 2.50e+03 1.45e-02 6.83e+00 pdb=" C08 QNG M 301 " -0.003 2.00e-02 2.50e+03 pdb=" C09 QNG M 301 " -0.002 2.00e-02 2.50e+03 pdb=" C10 QNG M 301 " -0.007 2.00e-02 2.50e+03 pdb=" C11 QNG M 301 " 0.000 2.00e-02 2.50e+03 pdb=" C12 QNG M 301 " 0.007 2.00e-02 2.50e+03 pdb=" C13 QNG M 301 " -0.029 2.00e-02 2.50e+03 pdb=" C16 QNG M 301 " -0.001 2.00e-02 2.50e+03 pdb=" C18 QNG M 301 " -0.005 2.00e-02 2.50e+03 pdb=" N14 QNG M 301 " 0.003 2.00e-02 2.50e+03 pdb=" N15 QNG M 301 " 0.002 2.00e-02 2.50e+03 pdb=" N17 QNG M 301 " 0.002 2.00e-02 2.50e+03 pdb="CL47 QNG M 301 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 QNG P 301 " 0.040 2.00e-02 2.50e+03 1.43e-02 6.60e+00 pdb=" C08 QNG P 301 " -0.004 2.00e-02 2.50e+03 pdb=" C09 QNG P 301 " -0.002 2.00e-02 2.50e+03 pdb=" C10 QNG P 301 " -0.006 2.00e-02 2.50e+03 pdb=" C11 QNG P 301 " 0.000 2.00e-02 2.50e+03 pdb=" C12 QNG P 301 " 0.008 2.00e-02 2.50e+03 pdb=" C13 QNG P 301 " -0.029 2.00e-02 2.50e+03 pdb=" C16 QNG P 301 " -0.001 2.00e-02 2.50e+03 pdb=" C18 QNG P 301 " -0.004 2.00e-02 2.50e+03 pdb=" N14 QNG P 301 " 0.003 2.00e-02 2.50e+03 pdb=" N15 QNG P 301 " 0.004 2.00e-02 2.50e+03 pdb=" N17 QNG P 301 " 0.001 2.00e-02 2.50e+03 pdb="CL47 QNG P 301 " -0.008 2.00e-02 2.50e+03 ... (remaining 5883 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 3041 2.70 - 3.25: 36403 3.25 - 3.80: 60099 3.80 - 4.35: 71870 4.35 - 4.90: 117619 Nonbonded interactions: 289032 Sorted by model distance: nonbonded pdb=" N GLU M 180 " pdb=" OE1 GLU M 180 " model vdw 2.147 3.120 nonbonded pdb=" N GLU C 180 " pdb=" OE1 GLU C 180 " model vdw 2.147 3.120 nonbonded pdb=" N GLU R 180 " pdb=" OE1 GLU R 180 " model vdw 2.147 3.120 nonbonded pdb=" N GLU D 180 " pdb=" OE1 GLU D 180 " model vdw 2.147 3.120 nonbonded pdb=" N GLU G 180 " pdb=" OE1 GLU G 180 " model vdw 2.147 3.120 ... (remaining 289027 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 301) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 30.510 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.190 33930 Z= 0.955 Angle : 1.639 26.830 46464 Z= 0.662 Chirality : 0.083 0.821 5010 Planarity : 0.007 0.050 5886 Dihedral : 20.559 148.865 13506 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.52 % Allowed : 19.37 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.12), residues: 4086 helix: 0.62 (0.09), residues: 2934 sheet: None (None), residues: 0 loop : -0.83 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 162 TYR 0.024 0.004 TYR A 164 PHE 0.007 0.003 PHE O 40 TRP 0.015 0.002 TRP M 133 HIS 0.009 0.003 HIS G 12 Details of bonding type rmsd/Z covalent geometry : bond 0.02137 / 0.96 (33930) covalent geometry : angle 1.63942 / 0.66 (46464) hydrogen bonds : bond 0.11596 / 7.79 ( 2106) hydrogen bonds : angle 5.54763 / 3.99 ( 6210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 879 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.9276 (t) cc_final: 0.9058 (p) REVERT: A 81 ASP cc_start: 0.9221 (m-30) cc_final: 0.9004 (m-30) REVERT: A 100 ARG cc_start: 0.8403 (mmm160) cc_final: 0.7944 (mmm160) REVERT: A 112 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8741 (tp-100) REVERT: B 51 ASP cc_start: 0.9265 (m-30) cc_final: 0.9015 (m-30) REVERT: B 82 ARG cc_start: 0.8981 (ttp80) cc_final: 0.8664 (tmt-80) REVERT: B 144 MET cc_start: 0.8817 (ppp) cc_final: 0.8608 (ppp) REVERT: B 173 ARG cc_start: 0.9041 (ttm110) cc_final: 0.8808 (mtm-85) REVERT: B 215 MET cc_start: 0.8728 (mtm) cc_final: 0.8522 (mtm) REVERT: C 13 GLN cc_start: 0.8722 (mt0) cc_final: 0.8344 (mt0) REVERT: C 25 LYS cc_start: 0.9250 (mtpp) cc_final: 0.8710 (mptt) REVERT: C 45 GLU cc_start: 0.8966 (tt0) cc_final: 0.8747 (tm-30) REVERT: C 131 LYS cc_start: 0.9551 (ttpp) cc_final: 0.9347 (ttpp) REVERT: C 144 MET cc_start: 0.9037 (ppp) cc_final: 0.8722 (ppp) REVERT: C 227 LYS cc_start: 0.8895 (mtmt) cc_final: 0.8617 (mtpp) REVERT: D 33 SER cc_start: 0.9217 (t) cc_final: 0.8764 (p) REVERT: D 112 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8681 (tp-100) REVERT: D 144 MET cc_start: 0.8975 (ppp) cc_final: 0.8367 (ppp) REVERT: D 212 GLU cc_start: 0.8243 (mp0) cc_final: 0.7944 (mp0) REVERT: E 51 ASP cc_start: 0.9245 (m-30) cc_final: 0.9039 (m-30) REVERT: E 82 ARG cc_start: 0.8927 (ttp80) cc_final: 0.8679 (tmt170) REVERT: E 144 MET cc_start: 0.8826 (ppp) cc_final: 0.8545 (ppp) REVERT: F 25 LYS cc_start: 0.9286 (mtpp) cc_final: 0.8818 (mptt) REVERT: F 118 MET cc_start: 0.9259 (mtp) cc_final: 0.9037 (mtp) REVERT: F 144 MET cc_start: 0.9023 (ppp) cc_final: 0.8693 (ppp) REVERT: F 227 LYS cc_start: 0.8963 (mtmt) cc_final: 0.8732 (mtpp) REVERT: G 170 LYS cc_start: 0.9306 (ttmm) cc_final: 0.9079 (ttpp) REVERT: H 100 ARG cc_start: 0.8858 (mmm160) cc_final: 0.8555 (mmm160) REVERT: H 144 MET cc_start: 0.8830 (ppp) cc_final: 0.8531 (ppp) REVERT: I 25 LYS cc_start: 0.9288 (mtpp) cc_final: 0.8648 (mptt) REVERT: I 118 MET cc_start: 0.9269 (mtp) cc_final: 0.9038 (mtp) REVERT: I 144 MET cc_start: 0.9056 (ppp) cc_final: 0.8702 (ppp) REVERT: I 227 LYS cc_start: 0.9032 (mtmt) cc_final: 0.8813 (mtpp) REVERT: J 33 SER cc_start: 0.9301 (t) cc_final: 0.9099 (p) REVERT: J 100 ARG cc_start: 0.8385 (mmm160) cc_final: 0.7999 (mmm160) REVERT: J 112 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8665 (tp-100) REVERT: J 158 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8904 (mtpt) REVERT: K 51 ASP cc_start: 0.9275 (m-30) cc_final: 0.9039 (m-30) REVERT: K 82 ARG cc_start: 0.8922 (ttp80) cc_final: 0.8699 (tmt-80) REVERT: K 144 MET cc_start: 0.8795 (ppp) cc_final: 0.8562 (ppp) REVERT: K 173 ARG cc_start: 0.9046 (ttm110) cc_final: 0.8832 (mtm-85) REVERT: K 215 MET cc_start: 0.8710 (mtm) cc_final: 0.8464 (mtm) REVERT: K 229 ARG cc_start: 0.8722 (ttm110) cc_final: 0.8514 (ttp-110) REVERT: L 25 LYS cc_start: 0.9255 (mtpp) cc_final: 0.8723 (mptt) REVERT: L 144 MET cc_start: 0.9035 (ppp) cc_final: 0.8720 (ppp) REVERT: L 227 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8616 (mtpp) REVERT: M 33 SER cc_start: 0.9245 (t) cc_final: 0.8837 (p) REVERT: M 112 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8682 (tp-100) REVERT: M 144 MET cc_start: 0.8950 (ppp) cc_final: 0.8732 (ppp) REVERT: M 158 LYS cc_start: 0.9139 (mtpt) cc_final: 0.8794 (mtpt) REVERT: M 212 GLU cc_start: 0.8203 (mp0) cc_final: 0.7940 (mp0) REVERT: N 51 ASP cc_start: 0.9255 (m-30) cc_final: 0.9051 (m-30) REVERT: N 82 ARG cc_start: 0.8985 (ttp80) cc_final: 0.8713 (tmt170) REVERT: N 144 MET cc_start: 0.8808 (ppp) cc_final: 0.8542 (ppp) REVERT: O 25 LYS cc_start: 0.9301 (mtpp) cc_final: 0.8816 (mptt) REVERT: O 118 MET cc_start: 0.9289 (mtp) cc_final: 0.9067 (mtp) REVERT: O 144 MET cc_start: 0.9036 (ppp) cc_final: 0.8712 (ppp) REVERT: O 227 LYS cc_start: 0.8969 (mtmt) cc_final: 0.8715 (mtpp) REVERT: P 112 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8685 (tp-100) REVERT: P 144 MET cc_start: 0.8946 (ppp) cc_final: 0.8729 (ppp) REVERT: P 170 LYS cc_start: 0.9313 (ttmm) cc_final: 0.9111 (ttpp) REVERT: Q 100 ARG cc_start: 0.8859 (mmm160) cc_final: 0.8551 (mmm160) REVERT: Q 144 MET cc_start: 0.8840 (ppp) cc_final: 0.8564 (ppp) REVERT: R 25 LYS cc_start: 0.9287 (mtpp) cc_final: 0.8662 (mptt) REVERT: R 118 MET cc_start: 0.9273 (mtp) cc_final: 0.9060 (mtp) REVERT: R 144 MET cc_start: 0.9043 (ppp) cc_final: 0.8702 (ppp) REVERT: R 227 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8617 (mtpp) outliers start: 18 outliers final: 14 residues processed: 897 average time/residue: 0.9750 time to fit residues: 989.3730 Evaluate side-chains 775 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 761 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain P residue 41 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain R residue 41 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN I 179 GLN L 183 ASN R 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.084792 restraints weight = 59292.923| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.56 r_work: 0.2851 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33930 Z= 0.152 Angle : 0.582 6.346 46464 Z= 0.278 Chirality : 0.040 0.169 5010 Planarity : 0.004 0.046 5886 Dihedral : 14.198 121.993 5582 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.86 % Allowed : 18.53 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.13), residues: 4086 helix: 2.19 (0.09), residues: 2934 sheet: None (None), residues: 0 loop : -0.47 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 173 TYR 0.011 0.001 TYR Q 169 PHE 0.009 0.001 PHE I 32 TRP 0.005 0.001 TRP J 184 HIS 0.003 0.001 HIS L 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (33930) covalent geometry : angle 0.58212 / 0.28 (46464) hydrogen bonds : bond 0.04395 / 2.93 ( 2106) hydrogen bonds : angle 4.08768 / 2.94 ( 6210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1009 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.9161 (t) cc_final: 0.8558 (p) REVERT: A 35 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8754 (mp0) REVERT: A 112 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8621 (tp-100) REVERT: A 140 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8969 (tttp) REVERT: A 144 MET cc_start: 0.8926 (ppp) cc_final: 0.8631 (ppp) REVERT: A 154 ARG cc_start: 0.8987 (mtt90) cc_final: 0.8660 (mtt90) REVERT: A 162 ARG cc_start: 0.8749 (tpp80) cc_final: 0.8369 (tpp80) REVERT: B 82 ARG cc_start: 0.9211 (ttp80) cc_final: 0.8712 (tmt-80) REVERT: B 144 MET cc_start: 0.8939 (ppp) cc_final: 0.8677 (ppp) REVERT: B 211 LEU cc_start: 0.9013 (tp) cc_final: 0.8682 (tm) REVERT: C 25 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8369 (mptt) REVERT: C 35 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8435 (mp0) REVERT: C 235 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7885 (pp-130) REVERT: D 33 SER cc_start: 0.9030 (t) cc_final: 0.8317 (p) REVERT: D 35 GLU cc_start: 0.9016 (mp0) cc_final: 0.8748 (mp0) REVERT: D 45 GLU cc_start: 0.8851 (tt0) cc_final: 0.8578 (tt0) REVERT: E 51 ASP cc_start: 0.9221 (m-30) cc_final: 0.9011 (m-30) REVERT: E 81 ASP cc_start: 0.9261 (m-30) cc_final: 0.9041 (m-30) REVERT: E 82 ARG cc_start: 0.9228 (ttp80) cc_final: 0.8739 (tmt170) REVERT: E 83 LEU cc_start: 0.9454 (mm) cc_final: 0.9246 (mt) REVERT: E 140 LYS cc_start: 0.8995 (tttp) cc_final: 0.8729 (tttp) REVERT: E 144 MET cc_start: 0.8903 (ppp) cc_final: 0.8580 (ppp) REVERT: E 162 ARG cc_start: 0.8915 (ttm-80) cc_final: 0.8582 (tpp80) REVERT: F 25 LYS cc_start: 0.8996 (mtpp) cc_final: 0.8412 (mptt) REVERT: F 35 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8525 (mp0) REVERT: F 45 GLU cc_start: 0.9057 (tt0) cc_final: 0.8466 (tm-30) REVERT: F 118 MET cc_start: 0.9083 (mtp) cc_final: 0.8684 (mtp) REVERT: F 140 LYS cc_start: 0.9238 (ttpp) cc_final: 0.8928 (ttpp) REVERT: F 235 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7920 (pp-130) REVERT: G 33 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8501 (p) REVERT: G 35 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8745 (mp0) REVERT: G 45 GLU cc_start: 0.8795 (tt0) cc_final: 0.8501 (tt0) REVERT: G 102 SER cc_start: 0.8930 (p) cc_final: 0.8719 (p) REVERT: G 144 MET cc_start: 0.8881 (ppp) cc_final: 0.8669 (ppp) REVERT: G 170 LYS cc_start: 0.9321 (ttmm) cc_final: 0.9098 (ttpp) REVERT: G 212 GLU cc_start: 0.8703 (mp0) cc_final: 0.8407 (mp0) REVERT: H 100 ARG cc_start: 0.8320 (mmm160) cc_final: 0.7933 (mmm160) REVERT: I 25 LYS cc_start: 0.9023 (mtpp) cc_final: 0.8418 (mptt) REVERT: I 45 GLU cc_start: 0.8969 (tt0) cc_final: 0.8408 (tm-30) REVERT: I 75 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8436 (mt-10) REVERT: I 98 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8821 (mm-30) REVERT: I 113 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8441 (mt-10) REVERT: I 118 MET cc_start: 0.9149 (mtp) cc_final: 0.8818 (mtp) REVERT: I 144 MET cc_start: 0.9025 (ppp) cc_final: 0.8618 (ppp) REVERT: J 33 SER cc_start: 0.9160 (t) cc_final: 0.8602 (p) REVERT: J 35 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8697 (mp0) REVERT: J 112 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8629 (tp-100) REVERT: J 154 ARG cc_start: 0.9026 (mtt90) cc_final: 0.8786 (mtt90) REVERT: J 158 LYS cc_start: 0.9361 (mtpt) cc_final: 0.9141 (mtpt) REVERT: J 162 ARG cc_start: 0.8748 (tpp80) cc_final: 0.8367 (tpp80) REVERT: K 82 ARG cc_start: 0.9214 (ttp80) cc_final: 0.8735 (tmt-80) REVERT: K 143 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.9127 (mtp85) REVERT: K 144 MET cc_start: 0.8952 (ppp) cc_final: 0.8689 (ppp) REVERT: K 211 LEU cc_start: 0.8973 (tp) cc_final: 0.8654 (tm) REVERT: L 25 LYS cc_start: 0.9010 (mtpp) cc_final: 0.8415 (mptt) REVERT: L 35 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8462 (mp0) REVERT: L 45 GLU cc_start: 0.8805 (tt0) cc_final: 0.8198 (tm-30) REVERT: L 235 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7877 (pp-130) REVERT: M 33 SER cc_start: 0.9037 (t) cc_final: 0.8322 (p) REVERT: M 35 GLU cc_start: 0.9028 (mp0) cc_final: 0.8755 (mp0) REVERT: M 45 GLU cc_start: 0.8864 (tt0) cc_final: 0.8571 (tt0) REVERT: M 112 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8708 (tp-100) REVERT: M 158 LYS cc_start: 0.9308 (mtpt) cc_final: 0.9031 (mtpt) REVERT: N 51 ASP cc_start: 0.9221 (m-30) cc_final: 0.9004 (m-30) REVERT: N 81 ASP cc_start: 0.9242 (m-30) cc_final: 0.9022 (m-30) REVERT: N 82 ARG cc_start: 0.9216 (ttp80) cc_final: 0.8758 (tmt170) REVERT: N 83 LEU cc_start: 0.9458 (mm) cc_final: 0.9250 (mt) REVERT: N 140 LYS cc_start: 0.8948 (tttp) cc_final: 0.8709 (tttp) REVERT: N 144 MET cc_start: 0.8899 (ppp) cc_final: 0.8583 (ppp) REVERT: N 162 ARG cc_start: 0.9017 (ttm-80) cc_final: 0.8594 (tpp80) REVERT: O 25 LYS cc_start: 0.8995 (mtpp) cc_final: 0.8390 (mptt) REVERT: O 35 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8561 (mp0) REVERT: O 45 GLU cc_start: 0.9015 (tt0) cc_final: 0.8421 (tm-30) REVERT: O 115 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9297 (pp) REVERT: O 140 LYS cc_start: 0.9231 (ttpp) cc_final: 0.8932 (ttpp) REVERT: O 235 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7931 (pp-130) REVERT: P 33 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8512 (p) REVERT: P 35 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8763 (mp0) REVERT: P 112 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8585 (tp-100) REVERT: P 170 LYS cc_start: 0.9317 (ttmm) cc_final: 0.9103 (ttpp) REVERT: P 212 GLU cc_start: 0.8681 (mp0) cc_final: 0.8403 (mp0) REVERT: Q 100 ARG cc_start: 0.8309 (mmm160) cc_final: 0.7926 (mmm160) REVERT: R 25 LYS cc_start: 0.9039 (mtpp) cc_final: 0.8413 (mptt) REVERT: R 45 GLU cc_start: 0.8984 (tt0) cc_final: 0.8315 (tm-30) REVERT: R 118 MET cc_start: 0.9147 (mtp) cc_final: 0.8840 (mtp) REVERT: R 144 MET cc_start: 0.9041 (ppp) cc_final: 0.8617 (ppp) REVERT: R 227 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8541 (mtpp) outliers start: 64 outliers final: 24 residues processed: 1016 average time/residue: 0.9473 time to fit residues: 1098.5024 Evaluate side-chains 949 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 916 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 121 ASN Chi-restraints excluded: chain K residue 143 ARG Chi-restraints excluded: chain L residue 235 MET Chi-restraints excluded: chain M residue 121 ASN Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 236 SER Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain O residue 235 MET Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 121 ASN Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 236 SER Chi-restraints excluded: chain R residue 33 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 147 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 205 optimal weight: 8.9990 chunk 377 optimal weight: 1.9990 chunk 362 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 228 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN D 74 ASN E 50 GLN L 183 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.105860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.085174 restraints weight = 59613.358| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.56 r_work: 0.2859 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33930 Z= 0.140 Angle : 0.554 6.168 46464 Z= 0.265 Chirality : 0.039 0.177 5010 Planarity : 0.004 0.045 5886 Dihedral : 12.457 112.923 5568 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.86 % Allowed : 19.40 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.13), residues: 4086 helix: 2.52 (0.09), residues: 2952 sheet: None (None), residues: 0 loop : -0.48 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 100 TYR 0.008 0.001 TYR G 169 PHE 0.010 0.001 PHE I 32 TRP 0.005 0.001 TRP R 184 HIS 0.003 0.001 HIS L 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (33930) covalent geometry : angle 0.55363 / 0.26 (46464) hydrogen bonds : bond 0.04192 / 2.79 ( 2106) hydrogen bonds : angle 3.96220 / 2.84 ( 6210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 981 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.9095 (t) cc_final: 0.8373 (p) REVERT: A 35 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8718 (mp0) REVERT: A 100 ARG cc_start: 0.8233 (mmm160) cc_final: 0.7567 (mmm160) REVERT: A 112 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8622 (tp-100) REVERT: A 140 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8969 (tttp) REVERT: A 144 MET cc_start: 0.8898 (ppp) cc_final: 0.8624 (ppp) REVERT: A 154 ARG cc_start: 0.9003 (mtt90) cc_final: 0.8633 (mtt90) REVERT: A 162 ARG cc_start: 0.8774 (tpp80) cc_final: 0.8444 (tpp-160) REVERT: B 79 GLU cc_start: 0.8506 (tp30) cc_final: 0.8029 (tm-30) REVERT: B 81 ASP cc_start: 0.9236 (m-30) cc_final: 0.9028 (m-30) REVERT: B 82 ARG cc_start: 0.9245 (ttp80) cc_final: 0.8710 (tmt170) REVERT: B 144 MET cc_start: 0.8890 (ppp) cc_final: 0.8657 (ppp) REVERT: B 162 ARG cc_start: 0.8888 (tpt-90) cc_final: 0.8579 (tpp-160) REVERT: C 18 ARG cc_start: 0.8991 (mmt180) cc_final: 0.8047 (mmp-170) REVERT: C 25 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8345 (mptt) REVERT: C 35 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8426 (mp0) REVERT: C 235 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7790 (pp-130) REVERT: D 35 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8748 (mp0) REVERT: D 45 GLU cc_start: 0.8854 (tt0) cc_final: 0.8550 (tt0) REVERT: D 96 MET cc_start: 0.8185 (ptt) cc_final: 0.7907 (ptp) REVERT: D 112 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8772 (tp-100) REVERT: E 81 ASP cc_start: 0.9282 (m-30) cc_final: 0.9016 (m-30) REVERT: E 82 ARG cc_start: 0.9243 (ttp80) cc_final: 0.8712 (tmt170) REVERT: E 83 LEU cc_start: 0.9431 (mm) cc_final: 0.9142 (mt) REVERT: E 140 LYS cc_start: 0.8988 (tttp) cc_final: 0.8702 (tttp) REVERT: E 144 MET cc_start: 0.8894 (ppp) cc_final: 0.8647 (ppp) REVERT: E 162 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8602 (tpp80) REVERT: F 25 LYS cc_start: 0.9041 (mtpp) cc_final: 0.8445 (mptt) REVERT: F 35 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8528 (mp0) REVERT: F 45 GLU cc_start: 0.8993 (tt0) cc_final: 0.8487 (tm-30) REVERT: F 115 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9283 (pp) REVERT: F 118 MET cc_start: 0.9154 (mtp) cc_final: 0.8798 (mtp) REVERT: F 235 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7834 (pp-130) REVERT: G 45 GLU cc_start: 0.8864 (tt0) cc_final: 0.8545 (tt0) REVERT: G 112 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8743 (tp-100) REVERT: G 170 LYS cc_start: 0.9307 (ttmm) cc_final: 0.9096 (ttpp) REVERT: G 212 GLU cc_start: 0.8688 (mp0) cc_final: 0.8419 (mp0) REVERT: H 100 ARG cc_start: 0.8386 (mmm160) cc_final: 0.7990 (mmm160) REVERT: I 25 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8381 (mptt) REVERT: I 45 GLU cc_start: 0.8918 (tt0) cc_final: 0.8364 (tm-30) REVERT: I 118 MET cc_start: 0.9128 (mtp) cc_final: 0.8797 (mtp) REVERT: I 144 MET cc_start: 0.9030 (ppp) cc_final: 0.8728 (ppp) REVERT: J 33 SER cc_start: 0.9101 (t) cc_final: 0.8328 (p) REVERT: J 35 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8768 (mp0) REVERT: J 100 ARG cc_start: 0.8223 (mmm160) cc_final: 0.7583 (mmm160) REVERT: J 112 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8625 (tp-100) REVERT: J 154 ARG cc_start: 0.9003 (mtt90) cc_final: 0.8662 (mtt90) REVERT: J 158 LYS cc_start: 0.9341 (mtpt) cc_final: 0.9112 (mtpt) REVERT: J 162 ARG cc_start: 0.8763 (tpp80) cc_final: 0.8426 (tpp-160) REVERT: K 82 ARG cc_start: 0.9247 (ttp80) cc_final: 0.8666 (tmt170) REVERT: K 144 MET cc_start: 0.8904 (ppp) cc_final: 0.8631 (ppp) REVERT: K 162 ARG cc_start: 0.8905 (tpt-90) cc_final: 0.8575 (tpp-160) REVERT: L 18 ARG cc_start: 0.8970 (mmt180) cc_final: 0.8031 (mmp-170) REVERT: L 25 LYS cc_start: 0.8985 (mtpp) cc_final: 0.8371 (mptt) REVERT: L 35 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8455 (mp0) REVERT: L 45 GLU cc_start: 0.8764 (tt0) cc_final: 0.8384 (tm-30) REVERT: L 235 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7789 (pp-130) REVERT: M 35 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8746 (mp0) REVERT: M 45 GLU cc_start: 0.8889 (tt0) cc_final: 0.8585 (tt0) REVERT: M 112 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8884 (tp-100) REVERT: M 158 LYS cc_start: 0.9300 (mtpt) cc_final: 0.9022 (mtpt) REVERT: N 81 ASP cc_start: 0.9278 (m-30) cc_final: 0.9015 (m-30) REVERT: N 82 ARG cc_start: 0.9230 (ttp80) cc_final: 0.8746 (tmt170) REVERT: N 83 LEU cc_start: 0.9434 (mm) cc_final: 0.9189 (mt) REVERT: N 140 LYS cc_start: 0.9000 (tttp) cc_final: 0.8728 (tttp) REVERT: N 144 MET cc_start: 0.8882 (ppp) cc_final: 0.8644 (ppp) REVERT: N 162 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8602 (tpp80) REVERT: O 25 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8391 (mptt) REVERT: O 35 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8541 (mp0) REVERT: O 45 GLU cc_start: 0.8942 (tt0) cc_final: 0.8471 (tm-30) REVERT: O 118 MET cc_start: 0.9165 (mtp) cc_final: 0.8840 (mtp) REVERT: O 235 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7859 (pp-130) REVERT: P 112 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8862 (tp-100) REVERT: P 170 LYS cc_start: 0.9309 (ttmm) cc_final: 0.9098 (ttpp) REVERT: P 212 GLU cc_start: 0.8673 (mp0) cc_final: 0.8419 (mp0) REVERT: Q 100 ARG cc_start: 0.8372 (mmm160) cc_final: 0.7973 (mmm160) REVERT: R 25 LYS cc_start: 0.9033 (mtpp) cc_final: 0.8359 (mptt) REVERT: R 35 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8496 (mp0) REVERT: R 45 GLU cc_start: 0.8978 (tt0) cc_final: 0.8342 (tm-30) REVERT: R 118 MET cc_start: 0.9152 (mtp) cc_final: 0.8847 (mtp) REVERT: R 144 MET cc_start: 0.9023 (ppp) cc_final: 0.8703 (ppp) REVERT: R 227 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8615 (mtpp) outliers start: 64 outliers final: 31 residues processed: 990 average time/residue: 0.9562 time to fit residues: 1075.6213 Evaluate side-chains 972 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 931 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 121 ASN Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain L residue 235 MET Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 121 ASN Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 162 ARG Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain O residue 235 MET Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 115 ILE Chi-restraints excluded: chain Q residue 199 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 228 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 341 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 chunk 297 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 305 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN E 50 GLN L 13 GLN L 183 ASN N 50 GLN O 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.106425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.085843 restraints weight = 59287.573| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.55 r_work: 0.2872 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33930 Z= 0.128 Angle : 0.548 7.598 46464 Z= 0.263 Chirality : 0.039 0.183 5010 Planarity : 0.004 0.043 5886 Dihedral : 11.267 109.841 5568 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.18 % Allowed : 19.98 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.13), residues: 4086 helix: 2.59 (0.09), residues: 2952 sheet: None (None), residues: 0 loop : -0.43 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 97 TYR 0.007 0.001 TYR D 169 PHE 0.008 0.001 PHE N 32 TRP 0.004 0.001 TRP M 184 HIS 0.003 0.001 HIS L 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (33930) covalent geometry : angle 0.54797 / 0.26 (46464) hydrogen bonds : bond 0.04020 / 2.68 ( 2106) hydrogen bonds : angle 3.88400 / 2.78 ( 6210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 970 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.9068 (t) cc_final: 0.8330 (p) REVERT: A 35 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8713 (mp0) REVERT: A 100 ARG cc_start: 0.8156 (mmm160) cc_final: 0.7571 (mmm160) REVERT: A 112 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8587 (tp-100) REVERT: A 140 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8952 (tttp) REVERT: A 144 MET cc_start: 0.8904 (ppp) cc_final: 0.8626 (ppp) REVERT: A 154 ARG cc_start: 0.8995 (mtt90) cc_final: 0.8663 (mtt90) REVERT: A 162 ARG cc_start: 0.8782 (tpp80) cc_final: 0.8442 (tpp-160) REVERT: B 79 GLU cc_start: 0.8525 (tp30) cc_final: 0.8035 (tm-30) REVERT: B 81 ASP cc_start: 0.9249 (m-30) cc_final: 0.9025 (m-30) REVERT: B 82 ARG cc_start: 0.9258 (ttp80) cc_final: 0.8683 (tmt170) REVERT: B 144 MET cc_start: 0.8903 (ppp) cc_final: 0.8665 (ppp) REVERT: B 162 ARG cc_start: 0.8846 (tpt-90) cc_final: 0.8604 (tpp80) REVERT: C 18 ARG cc_start: 0.8983 (mmt180) cc_final: 0.8059 (mmp-170) REVERT: C 25 LYS cc_start: 0.9026 (mtpp) cc_final: 0.8407 (mptt) REVERT: C 35 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8444 (mp0) REVERT: C 45 GLU cc_start: 0.8734 (tp30) cc_final: 0.8429 (tm-30) REVERT: C 140 LYS cc_start: 0.9203 (ttmm) cc_final: 0.8938 (ttpp) REVERT: C 235 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7823 (pp-130) REVERT: D 35 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8763 (pm20) REVERT: D 45 GLU cc_start: 0.8869 (tt0) cc_final: 0.8567 (tt0) REVERT: D 96 MET cc_start: 0.8135 (ptt) cc_final: 0.7860 (ptp) REVERT: D 112 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8768 (tp-100) REVERT: D 140 LYS cc_start: 0.9396 (tttm) cc_final: 0.9194 (tttp) REVERT: E 81 ASP cc_start: 0.9288 (m-30) cc_final: 0.9027 (m-30) REVERT: E 82 ARG cc_start: 0.9250 (ttp80) cc_final: 0.8716 (tmt170) REVERT: E 83 LEU cc_start: 0.9436 (mm) cc_final: 0.9144 (mt) REVERT: E 140 LYS cc_start: 0.8970 (tttp) cc_final: 0.8689 (tttp) REVERT: E 144 MET cc_start: 0.8855 (ppp) cc_final: 0.8616 (ppp) REVERT: E 162 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8567 (tpp80) REVERT: E 237 GLN cc_start: 0.9020 (tp40) cc_final: 0.8697 (mm110) REVERT: F 25 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8441 (mptt) REVERT: F 35 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8522 (mp0) REVERT: F 45 GLU cc_start: 0.9035 (tt0) cc_final: 0.8514 (tm-30) REVERT: F 115 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9280 (pp) REVERT: F 118 MET cc_start: 0.9158 (mtp) cc_final: 0.8839 (mtp) REVERT: F 140 LYS cc_start: 0.9107 (ttpp) cc_final: 0.8873 (ttmm) REVERT: F 235 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7788 (pp-130) REVERT: G 45 GLU cc_start: 0.8904 (tt0) cc_final: 0.8577 (tt0) REVERT: G 112 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8745 (tp-100) REVERT: G 170 LYS cc_start: 0.9296 (ttmm) cc_final: 0.9090 (ttpp) REVERT: G 212 GLU cc_start: 0.8680 (mp0) cc_final: 0.8419 (mp0) REVERT: H 81 ASP cc_start: 0.9326 (m-30) cc_final: 0.9008 (m-30) REVERT: H 100 ARG cc_start: 0.8383 (mmm160) cc_final: 0.8062 (mmm160) REVERT: H 144 MET cc_start: 0.8959 (ppp) cc_final: 0.8717 (pp-130) REVERT: I 25 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8384 (mptt) REVERT: I 45 GLU cc_start: 0.8916 (tt0) cc_final: 0.8456 (tm-30) REVERT: I 118 MET cc_start: 0.9121 (mtp) cc_final: 0.8772 (mtp) REVERT: I 144 MET cc_start: 0.9033 (ppp) cc_final: 0.8747 (ppp) REVERT: J 33 SER cc_start: 0.9063 (t) cc_final: 0.8317 (p) REVERT: J 35 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8668 (mp0) REVERT: J 100 ARG cc_start: 0.8134 (mmm160) cc_final: 0.7560 (mmm160) REVERT: J 112 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8597 (tp-100) REVERT: J 154 ARG cc_start: 0.8986 (mtt90) cc_final: 0.8635 (mtt90) REVERT: J 158 LYS cc_start: 0.9355 (mtpt) cc_final: 0.9124 (mtpt) REVERT: J 162 ARG cc_start: 0.8798 (tpp80) cc_final: 0.8446 (tpp-160) REVERT: K 79 GLU cc_start: 0.8603 (tp30) cc_final: 0.8143 (tm-30) REVERT: K 82 ARG cc_start: 0.9271 (ttp80) cc_final: 0.8712 (tmt170) REVERT: K 144 MET cc_start: 0.8910 (ppp) cc_final: 0.8663 (ppp) REVERT: K 162 ARG cc_start: 0.8880 (tpt-90) cc_final: 0.8563 (tpp-160) REVERT: L 13 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: L 18 ARG cc_start: 0.8964 (mmt180) cc_final: 0.8014 (mmp-170) REVERT: L 25 LYS cc_start: 0.9018 (mtpp) cc_final: 0.8425 (mptt) REVERT: L 35 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8416 (mp0) REVERT: L 45 GLU cc_start: 0.8858 (tt0) cc_final: 0.8432 (tm-30) REVERT: L 140 LYS cc_start: 0.9195 (ttmm) cc_final: 0.8927 (ttpp) REVERT: L 235 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7782 (pp-130) REVERT: M 35 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8788 (mp0) REVERT: M 45 GLU cc_start: 0.8868 (tt0) cc_final: 0.8546 (tt0) REVERT: M 112 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8884 (tp-100) REVERT: M 158 LYS cc_start: 0.9260 (mtpt) cc_final: 0.8983 (mtpt) REVERT: N 81 ASP cc_start: 0.9296 (m-30) cc_final: 0.9032 (m-30) REVERT: N 82 ARG cc_start: 0.9247 (ttp80) cc_final: 0.8721 (tmt170) REVERT: N 83 LEU cc_start: 0.9434 (mm) cc_final: 0.9139 (mt) REVERT: N 140 LYS cc_start: 0.8968 (tttp) cc_final: 0.8732 (tttp) REVERT: N 144 MET cc_start: 0.8848 (ppp) cc_final: 0.8591 (ppp) REVERT: N 162 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8579 (tpp80) REVERT: N 237 GLN cc_start: 0.9010 (tp40) cc_final: 0.8678 (mm110) REVERT: O 25 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8414 (mptt) REVERT: O 35 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8525 (mp0) REVERT: O 45 GLU cc_start: 0.8988 (tt0) cc_final: 0.8474 (tm-30) REVERT: O 118 MET cc_start: 0.9171 (mtp) cc_final: 0.8896 (mtp) REVERT: O 140 LYS cc_start: 0.9089 (ttpp) cc_final: 0.8851 (ttmm) REVERT: O 235 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7824 (pp-130) REVERT: P 45 GLU cc_start: 0.8909 (tt0) cc_final: 0.8392 (tm-30) REVERT: P 112 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8822 (tp-100) REVERT: P 170 LYS cc_start: 0.9305 (ttmm) cc_final: 0.9098 (ttpp) REVERT: P 212 GLU cc_start: 0.8666 (mp0) cc_final: 0.8417 (mp0) REVERT: Q 100 ARG cc_start: 0.8393 (mmm160) cc_final: 0.8003 (mmm160) REVERT: Q 237 GLN cc_start: 0.9108 (tp40) cc_final: 0.8745 (mm-40) REVERT: R 25 LYS cc_start: 0.9021 (mtpp) cc_final: 0.8337 (mptt) REVERT: R 35 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8481 (mp0) REVERT: R 45 GLU cc_start: 0.8981 (tt0) cc_final: 0.8442 (tm-30) REVERT: R 118 MET cc_start: 0.9166 (mtp) cc_final: 0.8855 (mtp) REVERT: R 144 MET cc_start: 0.9065 (ppp) cc_final: 0.8764 (ppp) REVERT: R 227 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8607 (mtpp) outliers start: 75 outliers final: 43 residues processed: 989 average time/residue: 0.9703 time to fit residues: 1091.6971 Evaluate side-chains 993 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 939 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain L residue 13 GLN Chi-restraints excluded: chain L residue 235 MET Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 121 ASN Chi-restraints excluded: chain N residue 162 ARG Chi-restraints excluded: chain N residue 236 SER Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain O residue 235 MET Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 154 ARG Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain Q residue 115 ILE Chi-restraints excluded: chain Q residue 199 LYS Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 199 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 1 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 192 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 350 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 338 optimal weight: 0.3980 chunk 240 optimal weight: 9.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN L 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.083865 restraints weight = 59822.864| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.57 r_work: 0.2838 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33930 Z= 0.202 Angle : 0.585 8.656 46464 Z= 0.281 Chirality : 0.041 0.183 5010 Planarity : 0.005 0.043 5886 Dihedral : 10.475 105.521 5568 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.24 % Allowed : 20.83 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.13), residues: 4086 helix: 2.56 (0.09), residues: 2934 sheet: None (None), residues: 0 loop : -0.32 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 97 TYR 0.009 0.002 TYR Q 169 PHE 0.009 0.001 PHE C 32 TRP 0.005 0.001 TRP P 80 HIS 0.003 0.001 HIS L 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (33930) covalent geometry : angle 0.58494 / 0.28 (46464) hydrogen bonds : bond 0.04362 / 2.91 ( 2106) hydrogen bonds : angle 4.00528 / 2.87 ( 6210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 953 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.9066 (t) cc_final: 0.8297 (p) REVERT: A 35 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8712 (mp0) REVERT: A 81 ASP cc_start: 0.9164 (m-30) cc_final: 0.8942 (m-30) REVERT: A 100 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7586 (mmm160) REVERT: A 112 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8603 (tp-100) REVERT: A 140 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8952 (tttp) REVERT: A 144 MET cc_start: 0.8952 (ppp) cc_final: 0.8625 (ppp) REVERT: A 154 ARG cc_start: 0.9030 (mtt90) cc_final: 0.8705 (mtt90) REVERT: A 162 ARG cc_start: 0.8769 (tpp80) cc_final: 0.8465 (tpp80) REVERT: B 79 GLU cc_start: 0.8501 (tp30) cc_final: 0.8017 (tm-30) REVERT: B 81 ASP cc_start: 0.9273 (m-30) cc_final: 0.9059 (m-30) REVERT: B 82 ARG cc_start: 0.9275 (ttp80) cc_final: 0.8671 (tmt170) REVERT: B 144 MET cc_start: 0.8917 (ppp) cc_final: 0.8620 (ppp) REVERT: B 162 ARG cc_start: 0.8882 (tpt-90) cc_final: 0.8588 (tpp-160) REVERT: C 18 ARG cc_start: 0.9024 (mmt180) cc_final: 0.8070 (mmp-170) REVERT: C 25 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8381 (mptt) REVERT: C 35 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8446 (mp0) REVERT: C 140 LYS cc_start: 0.9177 (ttmm) cc_final: 0.8931 (ttpp) REVERT: C 235 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7823 (pp-130) REVERT: D 35 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8759 (mp0) REVERT: D 45 GLU cc_start: 0.8959 (tt0) cc_final: 0.8637 (tt0) REVERT: D 112 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8823 (tp-100) REVERT: D 140 LYS cc_start: 0.9405 (tttm) cc_final: 0.9141 (tttm) REVERT: E 81 ASP cc_start: 0.9289 (m-30) cc_final: 0.9034 (m-30) REVERT: E 82 ARG cc_start: 0.9280 (ttp80) cc_final: 0.8718 (tmt170) REVERT: E 83 LEU cc_start: 0.9450 (mm) cc_final: 0.9155 (mt) REVERT: E 140 LYS cc_start: 0.8980 (tttp) cc_final: 0.8741 (tttp) REVERT: E 144 MET cc_start: 0.8842 (ppp) cc_final: 0.8550 (ppp) REVERT: E 162 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8613 (tpp80) REVERT: E 237 GLN cc_start: 0.8982 (tp40) cc_final: 0.8604 (mm110) REVERT: F 25 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8468 (mptt) REVERT: F 35 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8529 (mp0) REVERT: F 45 GLU cc_start: 0.9042 (tt0) cc_final: 0.8684 (tm-30) REVERT: F 115 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9265 (pp) REVERT: F 118 MET cc_start: 0.9196 (mtp) cc_final: 0.8914 (mtp) REVERT: F 140 LYS cc_start: 0.9100 (ttpp) cc_final: 0.8889 (ttmm) REVERT: F 235 MET cc_start: 0.8126 (tmt) cc_final: 0.7813 (pp-130) REVERT: G 45 GLU cc_start: 0.8991 (tt0) cc_final: 0.8663 (tt0) REVERT: G 112 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8750 (tp-100) REVERT: G 170 LYS cc_start: 0.9309 (ttmm) cc_final: 0.9097 (ttpp) REVERT: G 212 GLU cc_start: 0.8703 (mp0) cc_final: 0.8414 (mp0) REVERT: H 144 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8737 (pp-130) REVERT: I 25 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8396 (mptt) REVERT: I 45 GLU cc_start: 0.9003 (tt0) cc_final: 0.8461 (tm-30) REVERT: I 118 MET cc_start: 0.9154 (mtp) cc_final: 0.8844 (mtp) REVERT: I 144 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8806 (ppp) REVERT: J 33 SER cc_start: 0.9074 (t) cc_final: 0.8248 (p) REVERT: J 35 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8741 (mp0) REVERT: J 100 ARG cc_start: 0.8236 (mmm160) cc_final: 0.7586 (mmm160) REVERT: J 112 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8584 (tp-100) REVERT: J 154 ARG cc_start: 0.9022 (mtt90) cc_final: 0.8732 (mtt90) REVERT: J 162 ARG cc_start: 0.8790 (tpp80) cc_final: 0.8464 (tpp80) REVERT: K 79 GLU cc_start: 0.8617 (tp30) cc_final: 0.8169 (tm-30) REVERT: K 82 ARG cc_start: 0.9276 (ttp80) cc_final: 0.8671 (tmt170) REVERT: K 144 MET cc_start: 0.8912 (ppp) cc_final: 0.8616 (ppp) REVERT: K 162 ARG cc_start: 0.8866 (tpt-90) cc_final: 0.8628 (tpp80) REVERT: L 18 ARG cc_start: 0.9027 (mmt180) cc_final: 0.8063 (mmp-170) REVERT: L 25 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8362 (mptt) REVERT: L 35 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8449 (mp0) REVERT: L 45 GLU cc_start: 0.8918 (tt0) cc_final: 0.8570 (tm-30) REVERT: L 140 LYS cc_start: 0.9187 (ttmm) cc_final: 0.8943 (ttpp) REVERT: L 235 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7796 (pp-130) REVERT: M 35 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8756 (mp0) REVERT: M 45 GLU cc_start: 0.8925 (tt0) cc_final: 0.8603 (tt0) REVERT: M 112 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8664 (tp-100) REVERT: M 144 MET cc_start: 0.8912 (ppp) cc_final: 0.8565 (pp-130) REVERT: M 158 LYS cc_start: 0.9255 (mtpt) cc_final: 0.8988 (mtpt) REVERT: N 81 ASP cc_start: 0.9306 (m-30) cc_final: 0.9040 (m-30) REVERT: N 82 ARG cc_start: 0.9277 (ttp80) cc_final: 0.8719 (tmt170) REVERT: N 83 LEU cc_start: 0.9442 (mm) cc_final: 0.9136 (mt) REVERT: N 140 LYS cc_start: 0.8979 (tttp) cc_final: 0.8753 (tttp) REVERT: N 144 MET cc_start: 0.8856 (ppp) cc_final: 0.8568 (ppp) REVERT: N 162 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8618 (tpp80) REVERT: N 237 GLN cc_start: 0.8981 (tp40) cc_final: 0.8597 (mm110) REVERT: O 25 LYS cc_start: 0.9046 (mtpp) cc_final: 0.8424 (mptt) REVERT: O 35 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8559 (mp0) REVERT: O 45 GLU cc_start: 0.9024 (tt0) cc_final: 0.8659 (tm-30) REVERT: O 118 MET cc_start: 0.9176 (mtp) cc_final: 0.8895 (mtp) REVERT: O 235 MET cc_start: 0.8137 (tmt) cc_final: 0.7854 (pp-130) REVERT: P 45 GLU cc_start: 0.8934 (tt0) cc_final: 0.8437 (tm-30) REVERT: P 112 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8522 (tp-100) REVERT: P 170 LYS cc_start: 0.9320 (ttmm) cc_final: 0.9103 (ttpp) REVERT: P 212 GLU cc_start: 0.8684 (mp0) cc_final: 0.8405 (mp0) REVERT: R 25 LYS cc_start: 0.9073 (mtpp) cc_final: 0.8400 (mptt) REVERT: R 35 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8475 (mp0) REVERT: R 45 GLU cc_start: 0.9025 (tt0) cc_final: 0.8442 (tm-30) REVERT: R 118 MET cc_start: 0.9173 (mtp) cc_final: 0.8889 (mtp) REVERT: R 144 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8763 (ppp) outliers start: 77 outliers final: 42 residues processed: 970 average time/residue: 0.9532 time to fit residues: 1051.2659 Evaluate side-chains 1013 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 960 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain L residue 235 MET Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 162 ARG Chi-restraints excluded: chain N residue 236 SER Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 115 ILE Chi-restraints excluded: chain Q residue 236 SER Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 199 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 176 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 325 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 222 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN L 13 GLN L 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.107012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.086463 restraints weight = 59377.227| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.54 r_work: 0.2886 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33930 Z= 0.116 Angle : 0.558 9.507 46464 Z= 0.268 Chirality : 0.039 0.210 5010 Planarity : 0.005 0.054 5886 Dihedral : 9.798 105.933 5568 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.15 % Allowed : 21.26 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.13), residues: 4086 helix: 2.60 (0.09), residues: 2952 sheet: None (None), residues: 0 loop : -0.36 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 229 TYR 0.009 0.001 TYR K 130 PHE 0.007 0.001 PHE R 32 TRP 0.006 0.001 TRP D 133 HIS 0.002 0.000 HIS R 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (33930) covalent geometry : angle 0.55789 / 0.27 (46464) hydrogen bonds : bond 0.03808 / 2.54 ( 2106) hydrogen bonds : angle 3.86393 / 2.77 ( 6210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 996 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.9024 (t) cc_final: 0.8233 (p) REVERT: A 35 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8734 (mp0) REVERT: A 112 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8557 (tp-100) REVERT: A 144 MET cc_start: 0.8949 (ppp) cc_final: 0.8725 (ppp) REVERT: A 154 ARG cc_start: 0.9004 (mtt90) cc_final: 0.8268 (mtt90) REVERT: A 162 ARG cc_start: 0.8768 (tpp80) cc_final: 0.8478 (tpp80) REVERT: B 79 GLU cc_start: 0.8539 (tp30) cc_final: 0.8032 (tm-30) REVERT: B 81 ASP cc_start: 0.9274 (m-30) cc_final: 0.9025 (m-30) REVERT: B 82 ARG cc_start: 0.9278 (ttp80) cc_final: 0.8680 (tmt170) REVERT: B 144 MET cc_start: 0.8913 (ppp) cc_final: 0.8577 (ppp) REVERT: B 162 ARG cc_start: 0.8815 (tpt-90) cc_final: 0.8565 (tpp-160) REVERT: C 18 ARG cc_start: 0.8993 (mmt180) cc_final: 0.8201 (mmp-170) REVERT: C 25 LYS cc_start: 0.9020 (mtpp) cc_final: 0.8401 (mptt) REVERT: C 35 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8426 (mp0) REVERT: C 140 LYS cc_start: 0.9191 (ttmm) cc_final: 0.8870 (ttpt) REVERT: C 235 MET cc_start: 0.8026 (tmt) cc_final: 0.7761 (pp-130) REVERT: D 35 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8753 (pm20) REVERT: D 45 GLU cc_start: 0.8933 (tt0) cc_final: 0.8626 (tt0) REVERT: D 112 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8770 (tp-100) REVERT: D 140 LYS cc_start: 0.9378 (tttm) cc_final: 0.9171 (tttp) REVERT: E 81 ASP cc_start: 0.9283 (m-30) cc_final: 0.9018 (m-30) REVERT: E 82 ARG cc_start: 0.9286 (ttp80) cc_final: 0.8775 (tmt-80) REVERT: E 83 LEU cc_start: 0.9435 (mm) cc_final: 0.9149 (mt) REVERT: E 140 LYS cc_start: 0.8959 (tttp) cc_final: 0.8686 (tttp) REVERT: E 144 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8541 (ppp) REVERT: E 162 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8518 (tpp80) REVERT: E 237 GLN cc_start: 0.8956 (tp40) cc_final: 0.8572 (mm110) REVERT: F 25 LYS cc_start: 0.9027 (mtpp) cc_final: 0.8419 (mptt) REVERT: F 35 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8482 (mp0) REVERT: F 45 GLU cc_start: 0.9013 (tt0) cc_final: 0.8700 (tm-30) REVERT: F 115 ILE cc_start: 0.9501 (OUTLIER) cc_final: 0.9286 (pp) REVERT: F 118 MET cc_start: 0.9197 (mtp) cc_final: 0.8899 (mtp) REVERT: F 140 LYS cc_start: 0.9125 (ttpp) cc_final: 0.8880 (ttmm) REVERT: F 227 LYS cc_start: 0.9261 (mtpp) cc_final: 0.9010 (mtpp) REVERT: F 235 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7736 (pp-130) REVERT: G 35 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8857 (pm20) REVERT: G 45 GLU cc_start: 0.8940 (tt0) cc_final: 0.8539 (tm-30) REVERT: G 112 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8712 (tp-100) REVERT: G 162 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7469 (tpp-160) REVERT: G 170 LYS cc_start: 0.9289 (ttmm) cc_final: 0.9082 (ttpp) REVERT: G 212 GLU cc_start: 0.8667 (mp0) cc_final: 0.8414 (mp0) REVERT: H 81 ASP cc_start: 0.9354 (m-30) cc_final: 0.9048 (m-30) REVERT: H 140 LYS cc_start: 0.9099 (ttmm) cc_final: 0.8675 (tttp) REVERT: H 237 GLN cc_start: 0.8967 (tp40) cc_final: 0.8645 (mm110) REVERT: I 18 ARG cc_start: 0.9028 (mmt180) cc_final: 0.8040 (mmp-170) REVERT: I 25 LYS cc_start: 0.9028 (mtpp) cc_final: 0.8353 (mptt) REVERT: I 45 GLU cc_start: 0.8942 (tt0) cc_final: 0.8494 (tm-30) REVERT: I 75 GLU cc_start: 0.8641 (mt-10) cc_final: 0.7869 (mt-10) REVERT: I 79 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: I 118 MET cc_start: 0.9104 (mtp) cc_final: 0.8797 (mtp) REVERT: I 144 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8750 (ppp) REVERT: I 154 ARG cc_start: 0.8988 (mtt-85) cc_final: 0.8761 (mtt-85) REVERT: J 33 SER cc_start: 0.9022 (t) cc_final: 0.8187 (p) REVERT: J 35 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8789 (mp0) REVERT: J 112 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8557 (tp-100) REVERT: J 154 ARG cc_start: 0.8972 (mtt90) cc_final: 0.8259 (mtt90) REVERT: J 162 ARG cc_start: 0.8782 (tpp80) cc_final: 0.8474 (tpp80) REVERT: K 79 GLU cc_start: 0.8650 (tp30) cc_final: 0.8158 (tm-30) REVERT: K 82 ARG cc_start: 0.9267 (ttp80) cc_final: 0.8733 (tpt170) REVERT: K 100 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.8090 (mmm160) REVERT: K 144 MET cc_start: 0.8902 (ppp) cc_final: 0.8558 (ppp) REVERT: K 162 ARG cc_start: 0.8848 (tpt-90) cc_final: 0.8566 (tpp80) REVERT: L 18 ARG cc_start: 0.9005 (mmt180) cc_final: 0.8044 (mmp-170) REVERT: L 25 LYS cc_start: 0.9008 (mtpp) cc_final: 0.8391 (mptt) REVERT: L 35 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8417 (mp0) REVERT: L 45 GLU cc_start: 0.8864 (tt0) cc_final: 0.8526 (tm-30) REVERT: L 140 LYS cc_start: 0.9189 (ttmm) cc_final: 0.8911 (ttpp) REVERT: L 235 MET cc_start: 0.7995 (tmt) cc_final: 0.7730 (pp-130) REVERT: M 35 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8749 (pm20) REVERT: M 45 GLU cc_start: 0.8887 (tt0) cc_final: 0.8599 (tt0) REVERT: M 112 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8849 (tp-100) REVERT: M 158 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8998 (mtpt) REVERT: N 81 ASP cc_start: 0.9304 (m-30) cc_final: 0.9012 (m-30) REVERT: N 82 ARG cc_start: 0.9269 (ttp80) cc_final: 0.8745 (tmt-80) REVERT: N 83 LEU cc_start: 0.9424 (mm) cc_final: 0.9130 (mt) REVERT: N 140 LYS cc_start: 0.8968 (tttp) cc_final: 0.8711 (tttp) REVERT: N 144 MET cc_start: 0.8868 (ppp) cc_final: 0.8574 (ppp) REVERT: N 162 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8546 (tpp80) REVERT: N 237 GLN cc_start: 0.8948 (tp40) cc_final: 0.8558 (mm110) REVERT: O 25 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8389 (mptt) REVERT: O 35 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8509 (mp0) REVERT: O 45 GLU cc_start: 0.8989 (tt0) cc_final: 0.8672 (tm-30) REVERT: O 118 MET cc_start: 0.9136 (mtp) cc_final: 0.8897 (mtp) REVERT: O 140 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8865 (ttpp) REVERT: O 227 LYS cc_start: 0.9275 (mtpp) cc_final: 0.9050 (mtpp) REVERT: O 235 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7768 (pp-130) REVERT: P 35 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8892 (pm20) REVERT: P 45 GLU cc_start: 0.8921 (tt0) cc_final: 0.8500 (tm-30) REVERT: P 112 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8777 (tp-100) REVERT: P 162 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7462 (tpp-160) REVERT: P 170 LYS cc_start: 0.9299 (ttmm) cc_final: 0.9091 (ttpp) REVERT: P 192 GLN cc_start: 0.9307 (tt0) cc_final: 0.8988 (tt0) REVERT: P 212 GLU cc_start: 0.8653 (mp0) cc_final: 0.8413 (mp0) REVERT: Q 81 ASP cc_start: 0.9338 (m-30) cc_final: 0.9037 (m-30) REVERT: Q 140 LYS cc_start: 0.9122 (ttmm) cc_final: 0.8699 (tttp) REVERT: R 18 ARG cc_start: 0.9020 (mmt180) cc_final: 0.8045 (mmp-170) REVERT: R 25 LYS cc_start: 0.9039 (mtpp) cc_final: 0.8383 (mptt) REVERT: R 35 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8475 (mp0) REVERT: R 45 GLU cc_start: 0.8964 (tt0) cc_final: 0.8457 (tm-30) REVERT: R 118 MET cc_start: 0.9162 (mtp) cc_final: 0.8873 (mtp) REVERT: R 144 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8690 (ppp) REVERT: R 154 ARG cc_start: 0.8942 (mtt-85) cc_final: 0.8717 (mtt-85) outliers start: 74 outliers final: 40 residues processed: 1006 average time/residue: 0.9450 time to fit residues: 1079.7735 Evaluate side-chains 1024 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 971 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 162 ARG Chi-restraints excluded: chain N residue 236 SER Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 235 MET Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 162 ARG Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain Q residue 115 ILE Chi-restraints excluded: chain Q residue 236 SER Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 199 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 131 optimal weight: 7.9990 chunk 166 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 329 optimal weight: 6.9990 chunk 241 optimal weight: 7.9990 chunk 364 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN I 219 GLN L 183 ASN R 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.084483 restraints weight = 59914.474| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.55 r_work: 0.2849 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 33930 Z= 0.200 Angle : 0.599 10.106 46464 Z= 0.288 Chirality : 0.041 0.173 5010 Planarity : 0.005 0.057 5886 Dihedral : 9.565 103.023 5568 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.86 % Allowed : 22.19 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.13), residues: 4086 helix: 2.59 (0.09), residues: 2952 sheet: None (None), residues: 0 loop : -0.36 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 229 TYR 0.010 0.002 TYR C 130 PHE 0.009 0.001 PHE N 32 TRP 0.005 0.001 TRP G 80 HIS 0.003 0.001 HIS L 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (33930) covalent geometry : angle 0.59859 / 0.29 (46464) hydrogen bonds : bond 0.04189 / 2.79 ( 2106) hydrogen bonds : angle 3.97176 / 2.84 ( 6210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 958 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.9044 (t) cc_final: 0.8245 (p) REVERT: A 35 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8707 (mp0) REVERT: A 112 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8575 (tp-100) REVERT: A 140 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8954 (tttp) REVERT: A 144 MET cc_start: 0.8956 (ppp) cc_final: 0.8614 (ppp) REVERT: A 154 ARG cc_start: 0.9039 (mtt90) cc_final: 0.8555 (mtt90) REVERT: A 162 ARG cc_start: 0.8776 (tpp80) cc_final: 0.8465 (tpp80) REVERT: B 81 ASP cc_start: 0.9301 (m-30) cc_final: 0.9052 (m-30) REVERT: B 82 ARG cc_start: 0.9277 (ttp80) cc_final: 0.8616 (tmt170) REVERT: B 144 MET cc_start: 0.8909 (ppp) cc_final: 0.8561 (ppp) REVERT: B 162 ARG cc_start: 0.8888 (tpt-90) cc_final: 0.8543 (tpp-160) REVERT: C 18 ARG cc_start: 0.8868 (mmt180) cc_final: 0.8131 (mmt180) REVERT: C 25 LYS cc_start: 0.9009 (mtpp) cc_final: 0.8380 (mptt) REVERT: C 35 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8441 (mp0) REVERT: C 140 LYS cc_start: 0.9201 (ttmm) cc_final: 0.8967 (ttpp) REVERT: C 235 MET cc_start: 0.8046 (tmt) cc_final: 0.7764 (pp-130) REVERT: D 35 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8765 (mp0) REVERT: D 45 GLU cc_start: 0.8991 (tt0) cc_final: 0.8670 (tt0) REVERT: D 112 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8596 (tp-100) REVERT: D 140 LYS cc_start: 0.9401 (tttm) cc_final: 0.9177 (tttm) REVERT: D 144 MET cc_start: 0.8881 (ppp) cc_final: 0.8568 (pp-130) REVERT: E 81 ASP cc_start: 0.9288 (m-30) cc_final: 0.9042 (m-30) REVERT: E 82 ARG cc_start: 0.9288 (ttp80) cc_final: 0.8763 (tmt-80) REVERT: E 83 LEU cc_start: 0.9452 (mm) cc_final: 0.9165 (mt) REVERT: E 140 LYS cc_start: 0.8980 (tttp) cc_final: 0.8720 (tttp) REVERT: E 144 MET cc_start: 0.8823 (ppp) cc_final: 0.8500 (ppp) REVERT: E 162 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8460 (tpp80) REVERT: E 233 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7538 (tm-30) REVERT: E 237 GLN cc_start: 0.8948 (tp40) cc_final: 0.8411 (mm110) REVERT: F 25 LYS cc_start: 0.9043 (mtpp) cc_final: 0.8429 (mptt) REVERT: F 35 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8511 (mp0) REVERT: F 45 GLU cc_start: 0.9066 (tt0) cc_final: 0.8713 (tm-30) REVERT: F 115 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9257 (pp) REVERT: F 118 MET cc_start: 0.9211 (mtp) cc_final: 0.8911 (mtp) REVERT: F 140 LYS cc_start: 0.9142 (ttpp) cc_final: 0.8896 (ttmm) REVERT: F 227 LYS cc_start: 0.9311 (mtpp) cc_final: 0.9102 (mtpp) REVERT: F 235 MET cc_start: 0.8086 (tmt) cc_final: 0.7742 (pp-130) REVERT: G 45 GLU cc_start: 0.9021 (tt0) cc_final: 0.8657 (tm-30) REVERT: G 112 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8434 (tp-100) REVERT: G 154 ARG cc_start: 0.9036 (mtt90) cc_final: 0.8830 (mtt90) REVERT: G 162 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.7658 (tpp-160) REVERT: G 170 LYS cc_start: 0.9305 (ttmm) cc_final: 0.9095 (ttpp) REVERT: G 212 GLU cc_start: 0.8690 (mp0) cc_final: 0.8392 (mp0) REVERT: H 237 GLN cc_start: 0.8974 (tp40) cc_final: 0.8664 (mm110) REVERT: I 25 LYS cc_start: 0.9050 (mtpp) cc_final: 0.8380 (mptt) REVERT: I 45 GLU cc_start: 0.9023 (tt0) cc_final: 0.8536 (tm-30) REVERT: I 118 MET cc_start: 0.9111 (mtp) cc_final: 0.8805 (mtp) REVERT: I 144 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8722 (ppp) REVERT: J 33 SER cc_start: 0.9027 (t) cc_final: 0.8225 (p) REVERT: J 35 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8686 (mp0) REVERT: J 112 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8564 (tp-100) REVERT: J 154 ARG cc_start: 0.9032 (mtt90) cc_final: 0.8552 (mtt90) REVERT: J 162 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8461 (tpp80) REVERT: K 82 ARG cc_start: 0.9279 (ttp80) cc_final: 0.8697 (tpt170) REVERT: K 144 MET cc_start: 0.8901 (ppp) cc_final: 0.8558 (ppp) REVERT: K 162 ARG cc_start: 0.8868 (tpt-90) cc_final: 0.8573 (tpp80) REVERT: L 18 ARG cc_start: 0.9034 (mmt180) cc_final: 0.8077 (mmp-170) REVERT: L 25 LYS cc_start: 0.9023 (mtpp) cc_final: 0.8400 (mptt) REVERT: L 35 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8454 (mp0) REVERT: L 45 GLU cc_start: 0.8938 (tt0) cc_final: 0.8720 (tm-30) REVERT: L 140 LYS cc_start: 0.9201 (ttmm) cc_final: 0.8964 (ttpp) REVERT: L 235 MET cc_start: 0.8034 (tmt) cc_final: 0.7748 (pp-130) REVERT: M 35 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8770 (mp0) REVERT: M 45 GLU cc_start: 0.8942 (tt0) cc_final: 0.8629 (tt0) REVERT: M 112 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8656 (tp-100) REVERT: M 158 LYS cc_start: 0.9269 (mtpt) cc_final: 0.9020 (mtpt) REVERT: N 81 ASP cc_start: 0.9304 (m-30) cc_final: 0.9019 (m-30) REVERT: N 82 ARG cc_start: 0.9296 (ttp80) cc_final: 0.8762 (tmt-80) REVERT: N 83 LEU cc_start: 0.9439 (mm) cc_final: 0.9146 (mt) REVERT: N 140 LYS cc_start: 0.8989 (tttp) cc_final: 0.8761 (tttp) REVERT: N 144 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8538 (ppp) REVERT: N 162 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8565 (tpp80) REVERT: N 237 GLN cc_start: 0.8948 (tp40) cc_final: 0.8591 (mm110) REVERT: O 25 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8406 (mptt) REVERT: O 35 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8541 (mp0) REVERT: O 45 GLU cc_start: 0.9048 (tt0) cc_final: 0.8694 (tm-30) REVERT: O 118 MET cc_start: 0.9156 (mtp) cc_final: 0.8886 (mtp) REVERT: O 140 LYS cc_start: 0.9124 (ttmm) cc_final: 0.8870 (ttpp) REVERT: O 227 LYS cc_start: 0.9305 (mtpp) cc_final: 0.9102 (mtpp) REVERT: O 235 MET cc_start: 0.8122 (tmt) cc_final: 0.7787 (pp-130) REVERT: P 45 GLU cc_start: 0.8934 (tt0) cc_final: 0.8555 (tm-30) REVERT: P 112 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8508 (tp-100) REVERT: P 162 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.7660 (tpp-160) REVERT: P 170 LYS cc_start: 0.9327 (ttmm) cc_final: 0.9117 (ttpp) REVERT: P 212 GLU cc_start: 0.8670 (mp0) cc_final: 0.8366 (mp0) REVERT: Q 237 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8668 (mm110) REVERT: R 25 LYS cc_start: 0.9060 (mtpp) cc_final: 0.8389 (mptt) REVERT: R 35 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8485 (mp0) REVERT: R 45 GLU cc_start: 0.9030 (tt0) cc_final: 0.8472 (tm-30) REVERT: R 118 MET cc_start: 0.9184 (mtp) cc_final: 0.8874 (mtp) REVERT: R 144 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8652 (ppp) outliers start: 64 outliers final: 39 residues processed: 966 average time/residue: 0.9509 time to fit residues: 1042.5048 Evaluate side-chains 1024 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 973 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 144 MET Chi-restraints excluded: chain N residue 162 ARG Chi-restraints excluded: chain N residue 236 SER Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 162 ARG Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain Q residue 236 SER Chi-restraints excluded: chain Q residue 237 GLN Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 199 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 373 optimal weight: 2.9990 chunk 357 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 chunk 235 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 276 optimal weight: 7.9990 chunk 268 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 340 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN F 219 GLN I 179 GLN L 183 ASN Q 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.106033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.085345 restraints weight = 59543.438| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.54 r_work: 0.2866 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33930 Z= 0.144 Angle : 0.595 11.624 46464 Z= 0.285 Chirality : 0.040 0.192 5010 Planarity : 0.005 0.044 5886 Dihedral : 9.367 102.535 5568 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.95 % Allowed : 23.04 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.13), residues: 4086 helix: 2.59 (0.09), residues: 2952 sheet: None (None), residues: 0 loop : -0.36 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 97 TYR 0.010 0.001 TYR K 130 PHE 0.008 0.001 PHE D 32 TRP 0.004 0.001 TRP A 117 HIS 0.003 0.001 HIS I 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.14 (33930) covalent geometry : angle 0.59510 / 0.29 (46464) hydrogen bonds : bond 0.04037 / 2.69 ( 2106) hydrogen bonds : angle 3.93498 / 2.82 ( 6210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 991 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.9050 (t) cc_final: 0.8246 (p) REVERT: A 35 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8744 (mp0) REVERT: A 112 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8551 (tp-100) REVERT: A 140 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8972 (tttp) REVERT: A 144 MET cc_start: 0.8933 (ppp) cc_final: 0.8563 (ppp) REVERT: A 154 ARG cc_start: 0.9038 (mtt90) cc_final: 0.8290 (mtt90) REVERT: A 162 ARG cc_start: 0.8773 (tpp80) cc_final: 0.8465 (tpp80) REVERT: B 79 GLU cc_start: 0.8530 (tp30) cc_final: 0.8091 (tm-30) REVERT: B 81 ASP cc_start: 0.9322 (m-30) cc_final: 0.9058 (m-30) REVERT: B 82 ARG cc_start: 0.9255 (ttp80) cc_final: 0.8727 (tpt170) REVERT: B 144 MET cc_start: 0.8941 (ppp) cc_final: 0.8590 (ppp) REVERT: B 162 ARG cc_start: 0.8825 (tpt-90) cc_final: 0.8561 (tpp80) REVERT: C 18 ARG cc_start: 0.8898 (mmt180) cc_final: 0.8024 (mmt180) REVERT: C 25 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8430 (mptt) REVERT: C 35 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8418 (mp0) REVERT: C 140 LYS cc_start: 0.9224 (ttmm) cc_final: 0.8943 (ttpp) REVERT: C 235 MET cc_start: 0.8033 (tmt) cc_final: 0.7727 (pp-130) REVERT: D 45 GLU cc_start: 0.8997 (tt0) cc_final: 0.8676 (tt0) REVERT: D 112 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8608 (tp-100) REVERT: D 140 LYS cc_start: 0.9398 (tttm) cc_final: 0.9155 (tttm) REVERT: D 144 MET cc_start: 0.8836 (ppp) cc_final: 0.8494 (pp-130) REVERT: E 81 ASP cc_start: 0.9292 (m-30) cc_final: 0.9043 (m-30) REVERT: E 82 ARG cc_start: 0.9285 (ttp80) cc_final: 0.8759 (tmt-80) REVERT: E 83 LEU cc_start: 0.9451 (mm) cc_final: 0.9166 (mt) REVERT: E 140 LYS cc_start: 0.8975 (tttp) cc_final: 0.8730 (tttp) REVERT: E 144 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8486 (ppp) REVERT: E 162 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8414 (tpp-160) REVERT: E 233 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7546 (tm-30) REVERT: E 237 GLN cc_start: 0.8943 (tp40) cc_final: 0.8411 (mm110) REVERT: F 18 ARG cc_start: 0.9055 (mmt180) cc_final: 0.8088 (mmp-170) REVERT: F 25 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8421 (mptt) REVERT: F 35 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8509 (mp0) REVERT: F 45 GLU cc_start: 0.9037 (tt0) cc_final: 0.8730 (tm-30) REVERT: F 115 ILE cc_start: 0.9502 (OUTLIER) cc_final: 0.9245 (pp) REVERT: F 118 MET cc_start: 0.9225 (mtp) cc_final: 0.8935 (mtp) REVERT: F 140 LYS cc_start: 0.9139 (ttpp) cc_final: 0.8895 (ttmm) REVERT: F 227 LYS cc_start: 0.9306 (mtpp) cc_final: 0.9094 (mtpp) REVERT: F 235 MET cc_start: 0.8090 (tmt) cc_final: 0.7718 (pp-130) REVERT: G 45 GLU cc_start: 0.8999 (tt0) cc_final: 0.8691 (tm-30) REVERT: G 112 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8694 (tp-100) REVERT: G 162 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7504 (tpp-160) REVERT: G 170 LYS cc_start: 0.9301 (ttmm) cc_final: 0.9095 (ttpp) REVERT: G 212 GLU cc_start: 0.8684 (mp0) cc_final: 0.8405 (mp0) REVERT: H 81 ASP cc_start: 0.9357 (m-30) cc_final: 0.9055 (m-30) REVERT: H 237 GLN cc_start: 0.8931 (tp40) cc_final: 0.8610 (mm110) REVERT: I 18 ARG cc_start: 0.9021 (mmt180) cc_final: 0.8111 (mmp-170) REVERT: I 25 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8377 (mptt) REVERT: I 45 GLU cc_start: 0.8992 (tt0) cc_final: 0.8475 (tm-30) REVERT: I 75 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8410 (mt-10) REVERT: I 118 MET cc_start: 0.9126 (mtp) cc_final: 0.8800 (mtp) REVERT: I 144 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8660 (ppp) REVERT: J 112 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8560 (tp-100) REVERT: J 154 ARG cc_start: 0.9018 (mtt90) cc_final: 0.8247 (mtt90) REVERT: J 162 ARG cc_start: 0.8799 (tpp80) cc_final: 0.8479 (tpp80) REVERT: K 79 GLU cc_start: 0.8551 (tp30) cc_final: 0.8116 (tm-30) REVERT: K 82 ARG cc_start: 0.9253 (ttp80) cc_final: 0.8741 (tpt170) REVERT: K 100 ARG cc_start: 0.8393 (mmm-85) cc_final: 0.8157 (mmm160) REVERT: K 144 MET cc_start: 0.8902 (ppp) cc_final: 0.8562 (ppp) REVERT: K 162 ARG cc_start: 0.8840 (tpt-90) cc_final: 0.8503 (tpp-160) REVERT: L 18 ARG cc_start: 0.9023 (mmt180) cc_final: 0.8046 (mmp-170) REVERT: L 25 LYS cc_start: 0.9022 (mtpp) cc_final: 0.8418 (mptt) REVERT: L 35 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8441 (mp0) REVERT: L 45 GLU cc_start: 0.8925 (tt0) cc_final: 0.8715 (tm-30) REVERT: L 140 LYS cc_start: 0.9250 (ttmm) cc_final: 0.8977 (ttpp) REVERT: L 235 MET cc_start: 0.8035 (tmt) cc_final: 0.7729 (pp-130) REVERT: M 45 GLU cc_start: 0.8964 (tt0) cc_final: 0.8664 (tt0) REVERT: M 112 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8899 (tp-100) REVERT: M 144 MET cc_start: 0.8854 (ppp) cc_final: 0.8575 (pp-130) REVERT: M 158 LYS cc_start: 0.9255 (mtpt) cc_final: 0.9002 (mtpt) REVERT: N 81 ASP cc_start: 0.9311 (m-30) cc_final: 0.9034 (m-30) REVERT: N 82 ARG cc_start: 0.9299 (ttp80) cc_final: 0.8775 (tmt-80) REVERT: N 83 LEU cc_start: 0.9443 (mm) cc_final: 0.9141 (mt) REVERT: N 140 LYS cc_start: 0.8988 (tttp) cc_final: 0.8760 (tttp) REVERT: N 144 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8505 (ppp) REVERT: N 162 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8507 (tpp80) REVERT: N 237 GLN cc_start: 0.8933 (tp40) cc_final: 0.8585 (mm110) REVERT: O 18 ARG cc_start: 0.9072 (mmt180) cc_final: 0.8082 (mmp-170) REVERT: O 25 LYS cc_start: 0.9030 (mtpp) cc_final: 0.8398 (mptt) REVERT: O 35 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8537 (mp0) REVERT: O 45 GLU cc_start: 0.9028 (tt0) cc_final: 0.8717 (tm-30) REVERT: O 118 MET cc_start: 0.9134 (mtp) cc_final: 0.8860 (mtp) REVERT: O 140 LYS cc_start: 0.9126 (ttmm) cc_final: 0.8875 (ttpp) REVERT: O 227 LYS cc_start: 0.9292 (mtpp) cc_final: 0.9084 (mtpp) REVERT: O 235 MET cc_start: 0.8097 (tmt) cc_final: 0.7738 (pp-130) REVERT: P 45 GLU cc_start: 0.8932 (tt0) cc_final: 0.8560 (tm-30) REVERT: P 112 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8778 (tp-100) REVERT: P 162 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.7507 (tpp-160) REVERT: P 170 LYS cc_start: 0.9320 (ttmm) cc_final: 0.9112 (ttpp) REVERT: P 212 GLU cc_start: 0.8672 (mp0) cc_final: 0.8385 (mp0) REVERT: Q 229 ARG cc_start: 0.8779 (ttm-80) cc_final: 0.8129 (ttm-80) REVERT: R 18 ARG cc_start: 0.9011 (mmt180) cc_final: 0.8108 (mmp-170) REVERT: R 25 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8383 (mptt) REVERT: R 35 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8479 (mp0) REVERT: R 45 GLU cc_start: 0.8991 (tt0) cc_final: 0.8457 (tm-30) REVERT: R 118 MET cc_start: 0.9186 (mtp) cc_final: 0.8875 (mtp) REVERT: R 144 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8691 (ppp) outliers start: 67 outliers final: 41 residues processed: 999 average time/residue: 1.0168 time to fit residues: 1147.2835 Evaluate side-chains 1005 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 954 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 144 MET Chi-restraints excluded: chain N residue 162 ARG Chi-restraints excluded: chain N residue 236 SER Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 162 ARG Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain Q residue 236 SER Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 199 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 331 optimal weight: 0.9990 chunk 386 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 360 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 332 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 339 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN D 74 ASN L 183 ASN Q 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.085500 restraints weight = 59244.792| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.54 r_work: 0.2870 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33930 Z= 0.143 Angle : 0.599 11.784 46464 Z= 0.288 Chirality : 0.040 0.233 5010 Planarity : 0.005 0.047 5886 Dihedral : 9.203 101.610 5568 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.77 % Allowed : 23.18 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.13), residues: 4086 helix: 2.58 (0.09), residues: 2952 sheet: None (None), residues: 0 loop : -0.35 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 82 TYR 0.012 0.001 TYR K 130 PHE 0.008 0.001 PHE N 32 TRP 0.004 0.001 TRP D 117 HIS 0.002 0.001 HIS L 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (33930) covalent geometry : angle 0.59905 / 0.29 (46464) hydrogen bonds : bond 0.04015 / 2.67 ( 2106) hydrogen bonds : angle 3.94533 / 2.83 ( 6210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 976 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8555 (tp-100) REVERT: A 140 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8971 (tttp) REVERT: A 144 MET cc_start: 0.8919 (ppp) cc_final: 0.8556 (ppp) REVERT: A 154 ARG cc_start: 0.9042 (mtt90) cc_final: 0.8268 (mtt90) REVERT: A 162 ARG cc_start: 0.8782 (tpp80) cc_final: 0.8473 (tpp80) REVERT: B 79 GLU cc_start: 0.8537 (tp30) cc_final: 0.8088 (tm-30) REVERT: B 81 ASP cc_start: 0.9319 (m-30) cc_final: 0.9038 (m-30) REVERT: B 82 ARG cc_start: 0.9155 (ttp80) cc_final: 0.8728 (tpt170) REVERT: B 144 MET cc_start: 0.8938 (ppp) cc_final: 0.8573 (ppp) REVERT: C 25 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8424 (mptt) REVERT: C 35 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8422 (mp0) REVERT: C 140 LYS cc_start: 0.9232 (ttmm) cc_final: 0.8974 (ttpp) REVERT: C 235 MET cc_start: 0.8047 (tmt) cc_final: 0.7752 (pp-130) REVERT: D 35 GLU cc_start: 0.8815 (pm20) cc_final: 0.8512 (mp0) REVERT: D 45 GLU cc_start: 0.8997 (tt0) cc_final: 0.8676 (tt0) REVERT: D 112 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8644 (tp-100) REVERT: E 81 ASP cc_start: 0.9306 (m-30) cc_final: 0.9033 (m-30) REVERT: E 82 ARG cc_start: 0.9286 (ttp80) cc_final: 0.8758 (tmt-80) REVERT: E 83 LEU cc_start: 0.9468 (mm) cc_final: 0.9176 (mt) REVERT: E 140 LYS cc_start: 0.8968 (tttp) cc_final: 0.8705 (tttp) REVERT: E 144 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8467 (ppp) REVERT: E 162 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8390 (tpp-160) REVERT: E 233 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7560 (tm-30) REVERT: E 237 GLN cc_start: 0.8942 (tp40) cc_final: 0.8403 (mm110) REVERT: F 18 ARG cc_start: 0.9051 (mmt180) cc_final: 0.8080 (mmp-170) REVERT: F 25 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8426 (mptt) REVERT: F 35 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8525 (mp0) REVERT: F 45 GLU cc_start: 0.9037 (tt0) cc_final: 0.8736 (tm-30) REVERT: F 115 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9257 (pp) REVERT: F 118 MET cc_start: 0.9228 (mtp) cc_final: 0.8942 (mtp) REVERT: F 140 LYS cc_start: 0.9137 (ttpp) cc_final: 0.8904 (ttmm) REVERT: F 227 LYS cc_start: 0.9283 (mtpp) cc_final: 0.9076 (mtpp) REVERT: F 235 MET cc_start: 0.8127 (tmt) cc_final: 0.7780 (pp-130) REVERT: G 45 GLU cc_start: 0.8983 (tt0) cc_final: 0.8698 (tm-30) REVERT: G 112 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8687 (tp-100) REVERT: G 162 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.7502 (tpp-160) REVERT: G 170 LYS cc_start: 0.9303 (ttmm) cc_final: 0.9100 (ttpp) REVERT: G 212 GLU cc_start: 0.8690 (mp0) cc_final: 0.8415 (mp0) REVERT: H 81 ASP cc_start: 0.9348 (m-30) cc_final: 0.9042 (m-30) REVERT: H 237 GLN cc_start: 0.8912 (tp40) cc_final: 0.8605 (mm110) REVERT: I 18 ARG cc_start: 0.9014 (mmt180) cc_final: 0.8105 (mmp-170) REVERT: I 25 LYS cc_start: 0.9046 (mtpp) cc_final: 0.8376 (mptt) REVERT: I 45 GLU cc_start: 0.8975 (tt0) cc_final: 0.8460 (tm-30) REVERT: I 75 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8412 (mt-10) REVERT: I 118 MET cc_start: 0.9130 (mtp) cc_final: 0.8825 (mtp) REVERT: I 144 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8669 (ppp) REVERT: J 33 SER cc_start: 0.9097 (t) cc_final: 0.8140 (p) REVERT: J 35 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8615 (mp0) REVERT: J 112 GLN cc_start: 0.9150 (mm-40) cc_final: 0.8542 (tp-100) REVERT: J 154 ARG cc_start: 0.9028 (mtt90) cc_final: 0.8272 (mtt90) REVERT: J 162 ARG cc_start: 0.8780 (tpp80) cc_final: 0.8458 (tpp80) REVERT: K 79 GLU cc_start: 0.8549 (tp30) cc_final: 0.8119 (tm-30) REVERT: K 82 ARG cc_start: 0.9255 (ttp80) cc_final: 0.8755 (tpt170) REVERT: K 144 MET cc_start: 0.8933 (ppp) cc_final: 0.8562 (ppp) REVERT: K 162 ARG cc_start: 0.8790 (tpt-90) cc_final: 0.8577 (tpp-160) REVERT: L 25 LYS cc_start: 0.9019 (mtpp) cc_final: 0.8429 (mptt) REVERT: L 35 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8449 (mp0) REVERT: L 45 GLU cc_start: 0.8925 (tt0) cc_final: 0.8724 (tm-30) REVERT: L 140 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8940 (ttpp) REVERT: L 235 MET cc_start: 0.8123 (tmt) cc_final: 0.7809 (pp-130) REVERT: M 35 GLU cc_start: 0.8840 (pm20) cc_final: 0.8537 (mp0) REVERT: M 45 GLU cc_start: 0.8962 (tt0) cc_final: 0.8662 (tt0) REVERT: M 112 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8686 (tp-100) REVERT: M 158 LYS cc_start: 0.9251 (mtpt) cc_final: 0.9005 (mtpt) REVERT: N 81 ASP cc_start: 0.9313 (m-30) cc_final: 0.9058 (m-30) REVERT: N 82 ARG cc_start: 0.9292 (ttp80) cc_final: 0.8761 (tmt-80) REVERT: N 83 LEU cc_start: 0.9449 (mm) cc_final: 0.9158 (mt) REVERT: N 140 LYS cc_start: 0.8979 (tttp) cc_final: 0.8742 (tttp) REVERT: N 144 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8481 (ppp) REVERT: N 162 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8500 (tpp80) REVERT: N 233 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7532 (tm-30) REVERT: N 237 GLN cc_start: 0.8949 (tp40) cc_final: 0.8417 (mm110) REVERT: O 18 ARG cc_start: 0.9069 (mmt180) cc_final: 0.8087 (mmp-170) REVERT: O 25 LYS cc_start: 0.9028 (mtpp) cc_final: 0.8392 (mptt) REVERT: O 35 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8562 (mp0) REVERT: O 45 GLU cc_start: 0.9024 (tt0) cc_final: 0.8724 (tm-30) REVERT: O 118 MET cc_start: 0.9153 (mtp) cc_final: 0.8874 (mtp) REVERT: O 140 LYS cc_start: 0.9127 (ttmm) cc_final: 0.8883 (ttpp) REVERT: O 235 MET cc_start: 0.8139 (tmt) cc_final: 0.7798 (pp-130) REVERT: P 45 GLU cc_start: 0.8934 (tt0) cc_final: 0.8573 (tm-30) REVERT: P 112 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8782 (tp-100) REVERT: P 162 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7474 (tpp-160) REVERT: P 170 LYS cc_start: 0.9318 (ttmm) cc_final: 0.9109 (ttpp) REVERT: P 212 GLU cc_start: 0.8663 (mp0) cc_final: 0.8377 (mp0) REVERT: Q 112 GLN cc_start: 0.8746 (tp40) cc_final: 0.8372 (tp40) REVERT: R 18 ARG cc_start: 0.9012 (mmt180) cc_final: 0.8116 (mmp-170) REVERT: R 25 LYS cc_start: 0.9052 (mtpp) cc_final: 0.8380 (mptt) REVERT: R 35 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8493 (mp0) REVERT: R 45 GLU cc_start: 0.8987 (tt0) cc_final: 0.8454 (tm-30) REVERT: R 118 MET cc_start: 0.9176 (mtp) cc_final: 0.8864 (mtp) REVERT: R 144 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8687 (ppp) outliers start: 61 outliers final: 42 residues processed: 985 average time/residue: 1.0038 time to fit residues: 1119.2327 Evaluate side-chains 1003 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 951 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 144 MET Chi-restraints excluded: chain N residue 162 ARG Chi-restraints excluded: chain N residue 236 SER Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 162 ARG Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain Q residue 115 ILE Chi-restraints excluded: chain Q residue 236 SER Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 199 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 70 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 346 optimal weight: 4.9990 chunk 230 optimal weight: 8.9990 chunk 239 optimal weight: 0.0370 chunk 244 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 275 optimal weight: 0.2980 chunk 316 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN L 183 ASN R 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.086087 restraints weight = 59891.679| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.54 r_work: 0.2878 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33930 Z= 0.132 Angle : 0.611 12.326 46464 Z= 0.293 Chirality : 0.040 0.243 5010 Planarity : 0.005 0.056 5886 Dihedral : 9.082 101.446 5568 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.57 % Allowed : 23.68 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.13), residues: 4086 helix: 2.57 (0.09), residues: 2952 sheet: None (None), residues: 0 loop : -0.35 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 82 TYR 0.011 0.001 TYR K 130 PHE 0.007 0.001 PHE N 32 TRP 0.005 0.001 TRP J 184 HIS 0.002 0.000 HIS R 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (33930) covalent geometry : angle 0.61098 / 0.29 (46464) hydrogen bonds : bond 0.03932 / 2.62 ( 2106) hydrogen bonds : angle 3.93427 / 2.82 ( 6210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 966 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.9103 (t) cc_final: 0.8378 (p) REVERT: A 35 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8712 (mp0) REVERT: A 112 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8591 (tp-100) REVERT: A 140 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8967 (tttp) REVERT: A 144 MET cc_start: 0.8908 (ppp) cc_final: 0.8557 (ppp) REVERT: A 154 ARG cc_start: 0.9041 (mtt90) cc_final: 0.8257 (mtt90) REVERT: A 162 ARG cc_start: 0.8764 (tpp80) cc_final: 0.8458 (tpp80) REVERT: B 79 GLU cc_start: 0.8545 (tp30) cc_final: 0.8113 (tm-30) REVERT: B 81 ASP cc_start: 0.9313 (m-30) cc_final: 0.9034 (m-30) REVERT: B 82 ARG cc_start: 0.9155 (ttp80) cc_final: 0.8728 (tpt170) REVERT: B 144 MET cc_start: 0.8924 (ppp) cc_final: 0.8530 (ppp) REVERT: C 18 ARG cc_start: 0.8898 (mmt180) cc_final: 0.8009 (mmt180) REVERT: C 25 LYS cc_start: 0.9043 (mtpp) cc_final: 0.8427 (mptt) REVERT: C 35 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8420 (mp0) REVERT: C 140 LYS cc_start: 0.9200 (ttmm) cc_final: 0.8949 (ttpp) REVERT: C 235 MET cc_start: 0.8049 (tmt) cc_final: 0.7766 (pp-130) REVERT: D 45 GLU cc_start: 0.8991 (tt0) cc_final: 0.8682 (tt0) REVERT: D 112 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8614 (tp-100) REVERT: E 81 ASP cc_start: 0.9303 (m-30) cc_final: 0.9060 (m-30) REVERT: E 82 ARG cc_start: 0.9307 (ttp80) cc_final: 0.8770 (tmt-80) REVERT: E 83 LEU cc_start: 0.9467 (mm) cc_final: 0.9183 (mt) REVERT: E 140 LYS cc_start: 0.8971 (tttp) cc_final: 0.8728 (tttp) REVERT: E 144 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8450 (ppp) REVERT: E 162 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8423 (tpp-160) REVERT: E 233 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7565 (tm-30) REVERT: E 237 GLN cc_start: 0.8940 (tp40) cc_final: 0.8409 (mm110) REVERT: F 25 LYS cc_start: 0.9042 (mtpp) cc_final: 0.8424 (mptt) REVERT: F 35 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8546 (mp0) REVERT: F 45 GLU cc_start: 0.9031 (tt0) cc_final: 0.8739 (tm-30) REVERT: F 115 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9255 (pp) REVERT: F 118 MET cc_start: 0.9226 (mtp) cc_final: 0.8940 (mtp) REVERT: F 140 LYS cc_start: 0.9142 (ttpp) cc_final: 0.8931 (ttmm) REVERT: F 227 LYS cc_start: 0.9293 (mtpp) cc_final: 0.9088 (mtpp) REVERT: F 235 MET cc_start: 0.8123 (tmt) cc_final: 0.7761 (pp-130) REVERT: G 35 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8849 (pm20) REVERT: G 45 GLU cc_start: 0.8991 (tt0) cc_final: 0.8695 (tm-30) REVERT: G 112 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8718 (tp-100) REVERT: G 140 LYS cc_start: 0.9273 (ttpp) cc_final: 0.9007 (tttp) REVERT: G 154 ARG cc_start: 0.8990 (mtt90) cc_final: 0.8777 (mtt90) REVERT: G 162 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7493 (tpp-160) REVERT: G 170 LYS cc_start: 0.9295 (ttmm) cc_final: 0.9092 (ttpp) REVERT: G 212 GLU cc_start: 0.8690 (mp0) cc_final: 0.8416 (mp0) REVERT: H 81 ASP cc_start: 0.9353 (m-30) cc_final: 0.9046 (m-30) REVERT: H 162 ARG cc_start: 0.8677 (tpp80) cc_final: 0.7869 (tpp-160) REVERT: H 237 GLN cc_start: 0.8932 (tp40) cc_final: 0.8626 (mm110) REVERT: I 25 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8392 (mptt) REVERT: I 45 GLU cc_start: 0.8989 (tt0) cc_final: 0.8501 (tm-30) REVERT: I 75 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8428 (mt-10) REVERT: I 118 MET cc_start: 0.9133 (mtp) cc_final: 0.8838 (mtp) REVERT: I 144 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8663 (ppp) REVERT: I 229 ARG cc_start: 0.8884 (ttm-80) cc_final: 0.8665 (ttp80) REVERT: J 33 SER cc_start: 0.9073 (t) cc_final: 0.8356 (p) REVERT: J 35 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8713 (mp0) REVERT: J 112 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8579 (tp-100) REVERT: J 154 ARG cc_start: 0.9034 (mtt90) cc_final: 0.8285 (mtt90) REVERT: J 162 ARG cc_start: 0.8777 (tpp80) cc_final: 0.8457 (tpp80) REVERT: K 79 GLU cc_start: 0.8567 (tp30) cc_final: 0.8127 (tm-30) REVERT: K 82 ARG cc_start: 0.9187 (ttp80) cc_final: 0.8760 (tpt170) REVERT: K 100 ARG cc_start: 0.8322 (mmm-85) cc_final: 0.8085 (mmm160) REVERT: K 144 MET cc_start: 0.8930 (ppp) cc_final: 0.8550 (ppp) REVERT: K 162 ARG cc_start: 0.8808 (tpt-90) cc_final: 0.8580 (tpp80) REVERT: L 18 ARG cc_start: 0.9012 (mmt180) cc_final: 0.8036 (mmp-170) REVERT: L 25 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8423 (mptt) REVERT: L 35 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8450 (mp0) REVERT: L 45 GLU cc_start: 0.8922 (tt0) cc_final: 0.8716 (tm-30) REVERT: L 140 LYS cc_start: 0.9213 (ttmm) cc_final: 0.8977 (ttpp) REVERT: L 235 MET cc_start: 0.8116 (tmt) cc_final: 0.7811 (pp-130) REVERT: M 45 GLU cc_start: 0.8943 (tt0) cc_final: 0.8650 (tt0) REVERT: M 112 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8701 (tp-100) REVERT: M 132 ARG cc_start: 0.9336 (ttp-170) cc_final: 0.9126 (ttp-170) REVERT: M 144 MET cc_start: 0.8889 (ppp) cc_final: 0.8559 (pp-130) REVERT: M 158 LYS cc_start: 0.9254 (mtpt) cc_final: 0.9016 (mtpt) REVERT: N 81 ASP cc_start: 0.9313 (m-30) cc_final: 0.9056 (m-30) REVERT: N 82 ARG cc_start: 0.9296 (ttp80) cc_final: 0.8758 (tmt-80) REVERT: N 83 LEU cc_start: 0.9448 (mm) cc_final: 0.9148 (mt) REVERT: N 140 LYS cc_start: 0.8988 (tttp) cc_final: 0.8751 (tttp) REVERT: N 144 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8487 (ppp) REVERT: N 162 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8499 (tpp-160) REVERT: N 233 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7521 (tm-30) REVERT: N 237 GLN cc_start: 0.8919 (tp40) cc_final: 0.8392 (mm110) REVERT: O 25 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8403 (mptt) REVERT: O 35 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8568 (mp0) REVERT: O 45 GLU cc_start: 0.9003 (tt0) cc_final: 0.8697 (tm-30) REVERT: O 118 MET cc_start: 0.9143 (mtp) cc_final: 0.8871 (mtp) REVERT: O 140 LYS cc_start: 0.9124 (ttmm) cc_final: 0.8885 (ttpp) REVERT: O 235 MET cc_start: 0.8138 (tmt) cc_final: 0.7778 (pp-130) REVERT: P 35 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8859 (pm20) REVERT: P 45 GLU cc_start: 0.8934 (tt0) cc_final: 0.8573 (tm-30) REVERT: P 112 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8766 (tp-100) REVERT: P 140 LYS cc_start: 0.9274 (ttpp) cc_final: 0.8972 (tttp) REVERT: P 162 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7478 (tpp-160) REVERT: P 170 LYS cc_start: 0.9320 (ttmm) cc_final: 0.9110 (ttpp) REVERT: P 212 GLU cc_start: 0.8664 (mp0) cc_final: 0.8382 (mp0) REVERT: Q 81 ASP cc_start: 0.9351 (m-30) cc_final: 0.9059 (m-30) REVERT: Q 112 GLN cc_start: 0.8733 (tp40) cc_final: 0.8355 (tp40) REVERT: R 25 LYS cc_start: 0.9052 (mtpp) cc_final: 0.8379 (mptt) REVERT: R 35 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8496 (mp0) REVERT: R 45 GLU cc_start: 0.8970 (tt0) cc_final: 0.8436 (tm-30) REVERT: R 118 MET cc_start: 0.9174 (mtp) cc_final: 0.8891 (mtp) REVERT: R 144 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8654 (ppp) outliers start: 54 outliers final: 33 residues processed: 975 average time/residue: 0.9574 time to fit residues: 1060.9618 Evaluate side-chains 986 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 943 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 144 MET Chi-restraints excluded: chain N residue 162 ARG Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 162 ARG Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain Q residue 236 SER Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 199 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 142 optimal weight: 0.6980 chunk 364 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 258 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 332 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN L 183 ASN P 192 GLN Q 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.085627 restraints weight = 59526.406| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.55 r_work: 0.2874 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33930 Z= 0.151 Angle : 0.622 11.989 46464 Z= 0.299 Chirality : 0.042 0.526 5010 Planarity : 0.005 0.050 5886 Dihedral : 9.046 101.362 5568 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.51 % Allowed : 23.79 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.13), residues: 4086 helix: 2.56 (0.09), residues: 2952 sheet: None (None), residues: 0 loop : -0.35 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 82 TYR 0.012 0.001 TYR B 130 PHE 0.010 0.001 PHE H 168 TRP 0.005 0.001 TRP G 184 HIS 0.002 0.000 HIS G 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (33930) covalent geometry : angle 0.62171 / 0.30 (46464) hydrogen bonds : bond 0.03960 / 2.64 ( 2106) hydrogen bonds : angle 3.95419 / 2.84 ( 6210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21397.24 seconds wall clock time: 362 minutes 41.78 seconds (21761.78 seconds total)